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/7916117/working' mkdir: created directory `/scratch/stefan/7916117/working/protonate' Storing results in /scratch/stefan/7916117/finished Working in /scratch/stefan/7916117/working /scratch/stefan/7916117/working /scratch/stefan/7916117 /scratch/stefan/7916117/working/protonate /scratch/stefan/7916117/working /scratch/stefan/7916117 Precomputing protomers for all compounds (pH: 7.4) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: `/nfs/home/stefan/.install4j_new' and `/nfs/home/stefan/.install4j' are the same file 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 Jan 16, 2020 10:50:01 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 16, 2020 10:50:01 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. Jan 16, 2020 10:50:18 PM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. ph 7.4: 1078 protomers created Coalesing and merging protomers 1034 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1045 protomers after new stereo-center expansion /scratch/stefan/7916117/working /scratch/stefan/7916117 Bulk generating 3D conformations all protomers in /scratch/stefan/7916117/working/3D mkdir: created directory `/scratch/stefan/7916117/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7916117/working/protonate/xaaaaao-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' 1046 3D conformations generated for 1000 compounds Building REAL250005035450 mkdir: created directory `/scratch/stefan/7916117/working/building' mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035450' /scratch/stefan/7916117/working/building/REAL250005035450 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035450 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035450/0 /scratch/stefan/7916117/working/building/REAL250005035450 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1 `/scratch/stefan/7916117/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035450.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035450 none CC(C)(C)OC(=O)NCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 197, 156, 201, 126, 27, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 160, 126, 126, 26, 9, 8, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035450 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035450 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `/scratch/stefan/7916117/finished' Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035450/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035450 Building REAL250005035451 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035451' /scratch/stefan/7916117/working/building/REAL250005035451 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035451 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035451/0 /scratch/stefan/7916117/working/building/REAL250005035451 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/2 `/scratch/stefan/7916117/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005035451.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035451 none CC(C)(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 12, 25, 25, 25, 103, 103, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 12, 25, 103, 103, 103, 103, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 561 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035451 none CC(C)(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 78, 122, 45, 45, 45, 15, 7, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 125, 201, 201, 122, 122, 122, 122, 122, 122, 78, 78, 45, 15, 15, 7, 7, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 33, 34, 35, 36, 37, 38]) total number of confs: 990 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035451 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035451 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035451/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035451 Building REAL250005035452 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035452' /scratch/stefan/7916117/working/building/REAL250005035452 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035452 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035452/0 /scratch/stefan/7916117/working/building/REAL250005035452 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/3 `/scratch/stefan/7916117/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035452.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035452 none CCCCOC(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 186, 133, 109, 81, 41, 84, 41, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 186, 186, 133, 133, 84, 84, 84, 84, 40, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 857 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035452 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035452 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035452/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035452 Building REAL250005035453 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035453' /scratch/stefan/7916117/working/building/REAL250005035453 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035453 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035453/0 /scratch/stefan/7916117/working/building/REAL250005035453 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/4 `/scratch/stefan/7916117/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCC1CCCO1)NCCC1=NC(=O)O[N-]1) `REAL250005035453.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035453 none O=C(COCC1CCCO1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 98, 147, 174, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 108, 108, 174, 174, 201, 201, 201, 201, 201, 201, 201, 38, 8, 8, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 716 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035453 none O=C(COCC1CCCO1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 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, 47, 17, 7, 1, 1, 1, 1, 1, 1, 66, 66, 127, 127, 201, 201, 201, 201, 201, 47, 47, 7, 7, 1, 1, 1, 1, 1, 1, 1, 66, 127, 127, 127, 127] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34]) total number of confs: 651 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035453 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035453 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035453/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035453 Building REAL250005035454 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035454' /scratch/stefan/7916117/working/building/REAL250005035454 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035454 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035454/0 /scratch/stefan/7916117/working/building/REAL250005035454 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/5 `/scratch/stefan/7916117/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C=C([N+](=O)[O-])C=N1)NCCC1=NC(=O)O[N-]1) `REAL250005035454.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035454 none O=C(CCN1C=C([N+](=O)[O-])C=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 11, 11, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [37, 37, 37, 126, 146, 201, 201, 201, 201, 201, 201, 201, 15, 7, 1, 1, 1, 1, 1, 1, 1, 126, 126, 146, 146, 201, 201, 37, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 678 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035454 none O=C(CCN1C=C([N+](=O)[O-])C=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 11, 11, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [47, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 119, 121, 201, 201, 201, 201, 201, 12, 12, 8, 8, 1, 1, 47, 119, 119, 121, 121] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035454 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035454 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035454/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035454 Building REAL250005035455 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035455' /scratch/stefan/7916117/working/building/REAL250005035455 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035455 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035455/0 /scratch/stefan/7916117/working/building/REAL250005035455 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/6 `/scratch/stefan/7916117/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOC(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035455.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035455 none CC(C)CCOC(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 201, 167, 139, 112, 44, 109, 44, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 194, 194, 167, 167, 113, 113, 113, 109, 43, 8, 8, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 818 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035455 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035455 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035455/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035455 Building REAL250005035456 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035456' /scratch/stefan/7916117/working/building/REAL250005035456 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035456 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035456/0 /scratch/stefan/7916117/working/building/REAL250005035456 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/7 `/scratch/stefan/7916117/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCCC1=CC=CC=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035456.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035456 none O=C(COCCC1=CC=CC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [44, 44, 44, 100, 139, 173, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 113, 113, 173, 173, 201, 201, 201, 201, 201, 201, 201, 43, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035456 none O=C(COCCC1=CC=CC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [76, 49, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 76, 76, 134, 134, 201, 201, 201, 201, 201, 49, 49, 3, 3, 1, 1, 1, 1, 1, 1, 1, 76, 134, 134, 134, 134] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36]) total number of confs: 685 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035456 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035456 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035456/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035456 Building REAL250005035457 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035457' /scratch/stefan/7916117/working/building/REAL250005035457 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035457 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035457/0 /scratch/stefan/7916117/working/building/REAL250005035457 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/8 `/scratch/stefan/7916117/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OCC1CCCO1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035457.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035457 none CC(OCC1CCCO1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [114, 46, 115, 148, 169, 201, 201, 201, 201, 46, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 115, 114, 115, 115, 169, 169, 201, 201, 201, 201, 201, 201, 201, 45, 8, 8, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 714 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035457 none CC(OCC1CCCO1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 22, 7, 1, 1, 1, 1, 1, 1, 44, 76, 76, 76, 136, 136, 201, 201, 201, 201, 201, 44, 44, 44, 44, 7, 7, 1, 1, 1, 1, 1, 1, 1, 76, 136, 136, 136, 136] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37]) total number of confs: 668 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035457 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035457 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035457/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035457 Building REAL250005035458 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035458' /scratch/stefan/7916117/working/building/REAL250005035458 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035458 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035458/0 /scratch/stefan/7916117/working/building/REAL250005035458 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/9 `/scratch/stefan/7916117/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1) `REAL250005035458.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035458 none CC(C)CC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 201, 121, 121, 121, 83, 83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 201, 201, 201, 201, 191, 191, 83, 24, 24, 8, 8, 121] 201 rigid atoms, others: [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]) total number of confs: 765 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035458 none CC(C)CC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [8, 5, 8, 1, 1, 1, 1, 1, 4, 4, 4, 20, 31, 121, 121, 121, 121, 121, 1, 1, 8, 8, 8, 8, 8, 8, 8, 5, 5, 4, 20, 20, 31, 31, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 18, 19] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035458 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035458 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035458/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035458 Building REAL250005035459 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035459' /scratch/stefan/7916117/working/building/REAL250005035459 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035459 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035459/0 /scratch/stefan/7916117/working/building/REAL250005035459 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/10 `/scratch/stefan/7916117/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1[N+](=O)[O-]) `REAL250005035459.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035459 none CC1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 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, 102, 102, 102, 24, 8, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 175, 175, 175, 102, 24, 24, 8, 8] 175 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035459 none CC1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 11, 11, 11, 63, 89, 175, 175, 175, 175, 175, 1, 1, 2, 2, 2, 2, 2, 1, 11, 63, 63, 89, 89] 175 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035459 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035459 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035459/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035459 Building REAL250005035460 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035460' /scratch/stefan/7916117/working/building/REAL250005035460 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035460 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035460/0 /scratch/stefan/7916117/working/building/REAL250005035460 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/11 `/scratch/stefan/7916117/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2CC2)=N1) `REAL250005035460.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035460 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 39, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 12, 12, 1, 7, 29, 29, 39, 39, 1, 12, 12, 12, 12, 12] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035460 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [85, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 85, 137, 137, 137, 137, 201, 201, 137, 84, 24, 24, 8, 8, 137, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035460 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [44, 12, 44, 44, 109, 123, 201, 201, 201, 201, 201, 12, 12, 12, 1, 1, 1, 1, 12, 44, 109, 109, 123, 123, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 592 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035460 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035460 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035460/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035460 Building REAL250005035461 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035461' /scratch/stefan/7916117/working/building/REAL250005035461 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035461 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035461/0 /scratch/stefan/7916117/working/building/REAL250005035461 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/12 `/scratch/stefan/7916117/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOC(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035461.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035461 none C=CCCOC(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 139, 95, 86, 52, 86, 52, 52, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 139, 139, 86, 86, 86, 86, 52, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 907 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035461 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035461 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035461/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035461 Building REAL250005035462 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035462' /scratch/stefan/7916117/working/building/REAL250005035462 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035462 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035462/0 /scratch/stefan/7916117/working/building/REAL250005035462 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/13 `/scratch/stefan/7916117/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)NC2CC2)CC1) `REAL250005035462.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035462 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)NC2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 23, 27, 100, 100, 100, 100, 100, 1, 1, 4, 4, 4, 15, 15, 1, 1, 7, 23, 23, 27, 27, 4, 15, 15, 15, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 11, 12, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 233 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: REAL250005035462 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)NC2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 62, 17, 8, 1, 1, 1, 1, 1, 1, 1, 62, 99, 147, 147, 147, 201, 201, 99, 99, 62, 17, 17, 8, 8, 147, 201, 201, 201, 201, 201, 99, 99, 99, 99] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 720 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: REAL250005035462 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)NC2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 41, 41, 107, 110, 201, 201, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 15, 15, 41, 107, 107, 110, 110, 6, 1, 1, 1, 1, 1, 15, 15, 15, 15] 201 rigid atoms, others: [14, 15, 16, 17, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34]) total number of confs: 565 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035462 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035462 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035462/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035462 Building REAL250005035463 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035463' /scratch/stefan/7916117/working/building/REAL250005035463 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035463 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035463/0 /scratch/stefan/7916117/working/building/REAL250005035463 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/14 `/scratch/stefan/7916117/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C2C=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CN12) `REAL250005035463.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035463 none CC1=NN=C2C=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 137, 137, 137, 67, 67, 67, 22, 8, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 137, 137, 66, 22, 22, 8, 8, 137] 137 rigid atoms, others: [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]) total number of confs: 326 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035463 none CC1=NN=C2C=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 7, 7, 7, 45, 66, 137, 137, 137, 137, 137, 1, 1, 2, 2, 2, 1, 1, 7, 45, 45, 66, 66, 1] 137 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 393 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035463 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035463 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035463/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035463 Building REAL250005035464 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035464' /scratch/stefan/7916117/working/building/REAL250005035464 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035464 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035464/0 /scratch/stefan/7916117/working/building/REAL250005035464 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/15 `/scratch/stefan/7916117/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005035464.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035464 none CCC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 131, 131, 131, 131, 131, 44, 44, 44, 19, 8, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 201, 201, 131, 131, 131, 44, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 702 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035464 none CCC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 43, 131, 131, 131, 131, 131, 1, 8, 8, 8, 8, 8, 2, 2, 2, 7, 39, 39, 43, 43] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 18] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035464 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035464 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035464/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035464 Building REAL250005035465 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035465' /scratch/stefan/7916117/working/building/REAL250005035465 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035465 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035465/0 /scratch/stefan/7916117/working/building/REAL250005035465 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/16 `/scratch/stefan/7916117/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OCC1CCCCO1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035465.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035465 none CC(OCC1CCCCO1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 42, 91, 133, 172, 201, 201, 201, 201, 201, 42, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1, 95, 93, 95, 95, 172, 172, 201, 201, 201, 201, 201, 201, 201, 201, 201, 41, 8, 8, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 753 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035465 none CC(OCC1CCCCO1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 8, 1, 1, 1, 1, 1, 1, 1, 48, 83, 83, 83, 137, 137, 201, 201, 201, 201, 201, 48, 48, 48, 48, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 137, 137, 137, 137] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 27, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40]) total number of confs: 680 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035465 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035465 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035465/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035465 Building REAL250005035466 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035466' /scratch/stefan/7916117/working/building/REAL250005035466 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035466 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035466/0 /scratch/stefan/7916117/working/building/REAL250005035466 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/17 `/scratch/stefan/7916117/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C2OC(C(=O)NCCC3=NC(=O)O[N-]3)=CC2=CC=C1) `REAL250005035466.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035466 none CC1=C2OC(C(=O)NCCC3=NC(=O)O[N-]3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 1, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 142, 86, 86, 86, 23, 8, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 144, 144, 144, 144, 86, 23, 23, 8, 8, 144, 144, 144, 144] 144 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035466 none CC1=C2OC(C(=O)NCCC3=NC(=O)O[N-]3)=CC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 1, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 144 conformations in input total number of sets (complete confs): 144 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 13, 13, 13, 56, 78, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 2, 2, 2, 13, 56, 56, 78, 78, 1, 1, 1, 1] 144 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 16, 17, 18, 19, 20, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035466 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035466 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035466/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035466 Building REAL250005035467 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035467' /scratch/stefan/7916117/working/building/REAL250005035467 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035467 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035467/0 /scratch/stefan/7916117/working/building/REAL250005035467 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/18 `/scratch/stefan/7916117/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1CC1) `REAL250005035467.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035467 none CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 191, 191, 73, 73, 73, 23, 8, 1, 1, 1, 1, 1, 1, 1, 191, 191, 201, 201, 191, 191, 191, 191, 73, 23, 23, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL250005035467 none CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 11, 11, 11, 65, 83, 191, 191, 191, 191, 191, 1, 1, 3, 3, 2, 2, 2, 1, 11, 64, 64, 83, 83, 3, 3, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 494 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035467 none CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', '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, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 3, 3, 3, 3, 3, 19, 19, 19, 84, 100, 201, 201, 201, 201, 201, 1, 1, 1, 1, 3, 3, 3, 3, 19, 84, 84, 100, 100, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 539 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035467 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035467 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035467/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035467 Building REAL250005035468 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035468' /scratch/stefan/7916117/working/building/REAL250005035468 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035468 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035468/0 /scratch/stefan/7916117/working/building/REAL250005035468 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/19 `/scratch/stefan/7916117/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005035468.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035468 none NC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [190, 146, 190, 146, 146, 146, 76, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 146, 190, 190, 146, 146, 75, 24, 24, 8, 8] 190 rigid atoms, others: [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]) total number of confs: 492 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035468 none NC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [4, 1, 4, 1, 1, 1, 1, 1, 12, 12, 12, 62, 81, 146, 146, 146, 146, 146, 1, 5, 5, 1, 1, 12, 62, 62, 81, 81] 190 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 21, 22] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 23, 24, 25, 26, 27]) total number of confs: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035468 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035468 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035468/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035468 Building REAL250005035469 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035469' /scratch/stefan/7916117/working/building/REAL250005035469 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035469 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035469/0 /scratch/stefan/7916117/working/building/REAL250005035469 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/20 `/scratch/stefan/7916117/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035469.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035469 none CN(C)C1=CC=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 197, 201, 197, 197, 197, 197, 90, 90, 90, 24, 8, 1, 1, 1, 1, 1, 1, 1, 197, 201, 201, 201, 201, 201, 201, 197, 197, 90, 24, 24, 8, 8, 197] 201 rigid atoms, others: [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]) total number of confs: 451 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035469 none CN(C)C1=CC=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 34, 47, 197, 197, 197, 197, 197, 1, 5, 5, 5, 5, 5, 5, 1, 1, 10, 34, 34, 47, 47, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 33, 19, 26, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 376 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035469 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035469 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035469/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035469 Building REAL250005035470 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035470' /scratch/stefan/7916117/working/building/REAL250005035470 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035470 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035470/0 /scratch/stefan/7916117/working/building/REAL250005035470 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/21 `/scratch/stefan/7916117/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C)=C1C(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035470.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035470 none CC1=NN(C)C(C)=C1C(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 168, 80, 168, 80, 80, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 168, 168, 80, 24, 24, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 719 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: REAL250005035470 none CC1=NN(C)C(C)=C1C(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 4, 4, 16, 16, 16, 67, 90, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 16, 67, 67, 90, 90] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 568 number of broken/clashed sets: 152 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035470 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035470 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035470/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035470 Building REAL250005035471 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035471' /scratch/stefan/7916117/working/building/REAL250005035471 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035471 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035471/0 /scratch/stefan/7916117/working/building/REAL250005035471 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/22 `/scratch/stefan/7916117/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2COCC2=C1) `REAL250005035471.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035471 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2COCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 12, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 34, 59, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 34, 34, 59, 59, 1, 1, 1, 1, 1, 1, 1] 119 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) 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: REAL250005035471 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2COCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 12, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 21, 8, 1, 1, 1, 1, 1, 1, 1, 57, 119, 119, 118, 119, 119, 119, 119, 119, 56, 22, 22, 8, 8, 119, 119, 119, 119, 119, 119, 119] 119 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035471 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035471 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035471/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035471 Building REAL250005035472 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035472' /scratch/stefan/7916117/working/building/REAL250005035472 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035472 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035472/0 /scratch/stefan/7916117/working/building/REAL250005035472 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/23 `/scratch/stefan/7916117/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=NN=C2C=C1) `REAL250005035472.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035472 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=NN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 49, 79, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 49, 49, 79, 79, 1, 1, 1, 1] 147 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 447 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035472 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=NN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 22, 8, 1, 1, 1, 1, 1, 1, 1, 63, 147, 147, 147, 147, 147, 147, 147, 147, 63, 22, 22, 8, 8, 147, 147, 147, 147] 147 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035472 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035472 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035472/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035472 Building REAL250005035473 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035473' /scratch/stefan/7916117/working/building/REAL250005035473 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035473 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035473/0 /scratch/stefan/7916117/working/building/REAL250005035473 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/24 `/scratch/stefan/7916117/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1OCCO2) `REAL250005035473.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035473 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 52, 70, 166, 166, 166, 166, 166, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 52, 52, 70, 70, 1, 1, 1, 1, 1, 1, 1] 166 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) 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: REAL250005035473 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1OCCO2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 24, 8, 1, 1, 1, 1, 1, 1, 1, 66, 166, 166, 166, 166, 166, 166, 166, 166, 166, 66, 24, 24, 8, 8, 166, 166, 166, 166, 166, 166, 166] 166 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035473 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035473 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035473/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035473 Building REAL250005035474 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035474' /scratch/stefan/7916117/working/building/REAL250005035474 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035474 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035474/0 /scratch/stefan/7916117/working/building/REAL250005035474 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/25 `/scratch/stefan/7916117/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=C(F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035474.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035474 none CC(CC1=CC=C(F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [170, 66, 170, 201, 201, 201, 201, 201, 201, 201, 66, 66, 19, 8, 1, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 201, 201, 201, 201, 201, 201, 66, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 854 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035474 none CC(CC1=CC=C(F)C=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 26, 26, 26, 103, 112, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 26, 103, 103, 112, 112] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30] set([0, 32, 34, 35, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035474 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035474 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035474/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035474 Building REAL250005035475 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035475' /scratch/stefan/7916117/working/building/REAL250005035475 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035475 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035475/0 /scratch/stefan/7916117/working/building/REAL250005035475 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/26 `/scratch/stefan/7916117/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CC(F)=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035475.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035475 none CC(CC1=CC=CC(F)=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [114, 44, 114, 136, 201, 201, 201, 201, 201, 201, 44, 44, 17, 8, 1, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 136, 136, 201, 201, 201, 201, 44, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 708 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035475 none CC(CC1=CC=CC(F)=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 34, 34, 34, 111, 113, 201, 201, 201, 201, 201, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 34, 111, 111, 113, 113] 201 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: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035475 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035475 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035475/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035475 Building REAL250005035476 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035476' /scratch/stefan/7916117/working/building/REAL250005035476 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035476 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035476/0 /scratch/stefan/7916117/working/building/REAL250005035476 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/27 `/scratch/stefan/7916117/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)N1CCCC1=O) `REAL250005035476.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035476 none CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 1, 5, 17, 17, 17, 42, 42, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 5, 17, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1] 78 rigid atoms, others: [35, 34, 3, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL250005035476 none CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [75, 68, 75, 33, 33, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 68, 78, 78, 78, 78, 78, 75, 75, 75, 75, 75, 75, 75, 68, 32, 9, 9, 8, 8, 78, 78, 78, 78, 78, 78] 78 rigid atoms, others: [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, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 315 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035476 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035476 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035476/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035476 Building REAL250005035477 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035477' /scratch/stefan/7916117/working/building/REAL250005035477 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035477 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035477/0 /scratch/stefan/7916117/working/building/REAL250005035477 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/28 `/scratch/stefan/7916117/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(=O)OC1(C)C) `REAL250005035477.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035477 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(=O)OC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 100, 100, 100, 22, 8, 1, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 188, 188, 188, 188, 99, 22, 22, 8, 8, 188, 188, 188, 188, 188, 188] 188 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 427 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: REAL250005035477 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C(=O)OC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 54, 86, 188, 188, 188, 188, 188, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 54, 54, 86, 86, 2, 2, 2, 2, 2, 2] 188 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 537 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035477 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035477 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035477/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035477 Building REAL250005035478 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035478' /scratch/stefan/7916117/working/building/REAL250005035478 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035478 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035478/0 /scratch/stefan/7916117/working/building/REAL250005035478 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/29 `/scratch/stefan/7916117/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Cl)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035478.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035478 none COC1=CC(Cl)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 184, 184, 184, 163, 184, 184, 184, 68, 68, 68, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 184, 184, 184, 67, 20, 20, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 507 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035478 none COC1=CC(Cl)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 67, 79, 184, 184, 184, 184, 184, 3, 3, 3, 1, 1, 1, 12, 67, 67, 79, 79] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 455 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035478 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035478 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035478/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035478 Building REAL250005035479 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035479' /scratch/stefan/7916117/working/building/REAL250005035479 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035479 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035479/0 /scratch/stefan/7916117/working/building/REAL250005035479 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/30 `/scratch/stefan/7916117/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([N+](=O)[O-])C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035479.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035479 none CC1=CC=C([N+](=O)[O-])C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 192, 83, 192, 192, 192, 192, 192, 83, 83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 83, 192, 83, 25, 25, 8, 8] 192 rigid atoms, others: [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]) total number of confs: 593 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035479 none CC1=CC=C([N+](=O)[O-])C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 52, 86, 192, 192, 192, 192, 192, 2, 2, 2, 1, 1, 1, 9, 52, 52, 86, 86] 192 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 24, 25, 26] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035479 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035479 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035479/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035479 Building REAL250005035480 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035480' /scratch/stefan/7916117/working/building/REAL250005035480 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035480 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035480/0 /scratch/stefan/7916117/working/building/REAL250005035480 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/31 `/scratch/stefan/7916117/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C(C)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C) `REAL250005035480.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035480 none CCN1C(C)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 117, 117, 117, 117, 117, 60, 60, 60, 19, 8, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 117, 117, 117, 117, 60, 19, 19, 8, 8, 117, 117, 117] 201 rigid atoms, others: [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, 36]) total number of confs: 803 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035480 none CCN1C(C)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 9, 43, 53, 117, 117, 117, 117, 117, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 9, 43, 43, 53, 53, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 18, 19, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035480 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035480 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035480/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035480 Building REAL250005035481 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035481' /scratch/stefan/7916117/working/building/REAL250005035481 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035481 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035481/0 /scratch/stefan/7916117/working/building/REAL250005035481 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/32 `/scratch/stefan/7916117/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005035481.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035481 none CN1C=C(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 154, 82, 154, 82, 82, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 82, 19, 19, 8, 8, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 560 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035481 none CN1C=C(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 34, 34, 34, 94, 109, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 34, 94, 94, 109, 109, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 22, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 567 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035481 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035481 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035481/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035481 Building REAL250005035482 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035482' /scratch/stefan/7916117/working/building/REAL250005035482 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035482 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035482/0 /scratch/stefan/7916117/working/building/REAL250005035482 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/33 `/scratch/stefan/7916117/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC([N+](=O)[O-])=CN1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035482.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035482 none CC1=NC([N+](=O)[O-])=CN1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 11, 11, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 118, 35, 35, 35, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 118, 118, 35, 15, 15, 7, 7] 201 rigid atoms, others: [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]) 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: REAL250005035482 none CC1=NC([N+](=O)[O-])=CN1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 11, 11, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 33, 33, 33, 104, 106, 201, 201, 201, 201, 201, 2, 2, 2, 1, 8, 8, 33, 104, 104, 106, 106] 201 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 24] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 570 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035482 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035482 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035482/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035482 Building REAL250005035483 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035483' /scratch/stefan/7916117/working/building/REAL250005035483 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035483 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035483/0 /scratch/stefan/7916117/working/building/REAL250005035483 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/34 `/scratch/stefan/7916117/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035483.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035483 none C[NH+](C)CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 189, 118, 85, 170, 170, 85, 85, 85, 17, 8, 1, 1, 1, 1, 1, 1, 1, 170, 170, 189, 189, 189, 189, 189, 189, 189, 189, 170, 170, 85, 17, 17, 8, 8, 170, 170] 189 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 975 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035483 none C[NH+](C)CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 43, 57, 170, 170, 170, 170, 170, 1, 1, 5, 5, 5, 5, 5, 5, 4, 4, 1, 1, 7, 43, 43, 57, 57, 1, 1] 189 rigid atoms, others: [4, 5, 6, 7, 8, 9, 20, 21, 38, 37, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035483 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035483 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035483/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035483 Building REAL250005035484 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035484' /scratch/stefan/7916117/working/building/REAL250005035484 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035484 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035484/0 /scratch/stefan/7916117/working/building/REAL250005035484 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/35 `/scratch/stefan/7916117/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(Cl)=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035484.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035484 none CC1=NOC(Cl)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 16, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 146, 43, 43, 43, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 146, 146, 43, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035484 none CC1=NOC(Cl)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'Cl', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 16, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 30, 30, 30, 95, 97, 201, 201, 201, 201, 201, 2, 2, 2, 7, 7, 30, 95, 95, 97, 97] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 532 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035484 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035484 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035484/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035484 Building REAL250005035485 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035485' /scratch/stefan/7916117/working/building/REAL250005035485 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035485 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035485/0 /scratch/stefan/7916117/working/building/REAL250005035485 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/36 `/scratch/stefan/7916117/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=CC=N1)NCCC1=NC(=O)O[N-]1) `REAL250005035485.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035485 none O=C(CCC1=CC=CC=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 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: [49, 49, 49, 146, 164, 201, 201, 201, 201, 201, 18, 7, 1, 1, 1, 1, 1, 1, 1, 146, 146, 164, 164, 201, 201, 201, 201, 49, 18, 18, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 746 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035485 none O=C(CCC1=CC=CC=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 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: [51, 12, 6, 1, 1, 1, 1, 1, 1, 1, 51, 51, 120, 127, 201, 201, 201, 201, 201, 12, 12, 6, 6, 1, 1, 1, 1, 51, 123, 123, 129, 128] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035485 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035485 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035485/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035485 Building REAL250005035486 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035486' /scratch/stefan/7916117/working/building/REAL250005035486 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035486 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035486/0 /scratch/stefan/7916117/working/building/REAL250005035486 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/37 `/scratch/stefan/7916117/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1CCCCC1) `REAL250005035486.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035486 none CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 45, 45, 45, 103, 103, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 15, 15, 45, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 40, 41, 39, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 577 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035486 none CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 115, 40, 40, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 155, 201, 201, 201, 201, 201, 155, 155, 155, 151, 123, 123, 39, 8, 8, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 803 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035486 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035486 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035486/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035486 Building REAL250005035487 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035487' /scratch/stefan/7916117/working/building/REAL250005035487 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035487 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035487/0 /scratch/stefan/7916117/working/building/REAL250005035487 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/38 `/scratch/stefan/7916117/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=N1) `REAL250005035487.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035487 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 69, 94, 176, 176, 176, 176, 176, 1, 1, 1, 1, 1, 1, 1, 13, 69, 69, 94, 94, 1, 1, 1] 176 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) 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: REAL250005035487 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 24, 8, 1, 1, 1, 1, 1, 1, 1, 98, 176, 176, 176, 176, 176, 176, 98, 24, 24, 8, 8, 176, 176, 176] 176 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035487 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035487 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035487/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035487 Building REAL250005035488 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035488' /scratch/stefan/7916117/working/building/REAL250005035488 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035488 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035488/0 /scratch/stefan/7916117/working/building/REAL250005035488 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/39 `/scratch/stefan/7916117/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035488.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035488 none CCC(NC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [105, 93, 34, 93, 154, 191, 191, 191, 191, 191, 34, 34, 14, 7, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 93, 154, 191, 191, 191, 191, 191, 34, 14, 14, 7, 7] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 887 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: REAL250005035488 none CCC(NC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [17, 11, 6, 1, 1, 1, 1, 1, 1, 1, 11, 36, 36, 36, 102, 102, 191, 191, 191, 191, 191, 20, 20, 20, 20, 20, 11, 6, 1, 1, 1, 1, 1, 36, 102, 102, 102, 102] 201 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]) total number of confs: 606 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035488 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035488 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035488/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035488 Building REAL250005035489 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035489' /scratch/stefan/7916117/working/building/REAL250005035489 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035489 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035489/0 /scratch/stefan/7916117/working/building/REAL250005035489 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/40 `/scratch/stefan/7916117/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035489.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035489 none CC1=CC=C(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 193, 201, 201, 142, 72, 142, 72, 72, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 72, 19, 19, 8, 8, 201, 201] 201 rigid atoms, others: [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]) 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: REAL250005035489 none CC1=CC=C(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 11, 11, 35, 35, 35, 98, 108, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 35, 98, 98, 108, 108, 1, 1] 201 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: 575 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035489 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035489 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035489/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035489 Building REAL250005035490 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035490' /scratch/stefan/7916117/working/building/REAL250005035490 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035490 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035490/0 /scratch/stefan/7916117/working/building/REAL250005035490 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/41 `/scratch/stefan/7916117/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C(F)(F)F)CC1) `REAL250005035490.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035490 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 15, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 45, 86, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 7, 45, 45, 86, 86, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 16, 17, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 18, 19, 20, 21, 22]) total number of confs: 563 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: REAL250005035490 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 15, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [93, 93, 23, 8, 1, 1, 1, 1, 1, 1, 1, 93, 201, 201, 201, 201, 201, 201, 93, 23, 23, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 602 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035490 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035490 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035490/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035490 Building REAL250005035491 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035491' /scratch/stefan/7916117/working/building/REAL250005035491 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035491 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035491/0 /scratch/stefan/7916117/working/building/REAL250005035491 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/42 `/scratch/stefan/7916117/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005035491.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035491 none CN1C=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 116, 48, 48, 48, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 116, 116, 48, 17, 17, 8, 8, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 604 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035491 none CN1C=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 8, 23, 23, 23, 86, 92, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 8, 8, 23, 86, 86, 92, 92, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 21, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035491 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035491 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035491/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035491 Building REAL250005035492 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035492' /scratch/stefan/7916117/working/building/REAL250005035492 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035492 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035492/0 /scratch/stefan/7916117/working/building/REAL250005035492 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/43 `/scratch/stefan/7916117/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035492.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035492 none CCN1N=C(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 147, 147, 147, 147, 147, 147, 83, 83, 83, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 147, 147, 147, 147, 83, 23, 23, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 684 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035492 none CCN1N=C(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 44, 60, 147, 147, 147, 147, 147, 6, 6, 6, 6, 6, 2, 2, 2, 1, 10, 44, 44, 60, 60] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 391 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035492 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035492 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035492/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035492 Building REAL250005035493 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035493' /scratch/stefan/7916117/working/building/REAL250005035493 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035493 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035493/0 /scratch/stefan/7916117/working/building/REAL250005035493 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/44 `/scratch/stefan/7916117/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=N1) `REAL250005035493.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035493 none NC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 51, 51, 51, 20, 8, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 129, 129, 51, 20, 20, 8, 8, 129] 129 rigid atoms, others: [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]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035493 none NC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 31, 53, 129, 129, 129, 129, 129, 1, 1, 1, 1, 2, 2, 1, 5, 31, 31, 53, 53, 1] 129 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 21, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035493 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035493 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035493/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035493 Building REAL250005035494 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035494' /scratch/stefan/7916117/working/building/REAL250005035494 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035494 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035494/0 /scratch/stefan/7916117/working/building/REAL250005035494 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/45 `/scratch/stefan/7916117/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC([N+](=O)[O-])=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035494.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035494 none CC1=CC([N+](=O)[O-])=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 154, 157, 157, 157, 157, 157, 92, 92, 92, 24, 8, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 157, 157, 92, 24, 24, 8, 8] 157 rigid atoms, others: [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]) total number of confs: 402 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035494 none CC1=CC([N+](=O)[O-])=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 56, 94, 157, 157, 157, 157, 157, 2, 2, 2, 1, 1, 1, 10, 56, 56, 94, 94] 157 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 514 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035494 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035494 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035494/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035494 Building REAL250005035495 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035495' /scratch/stefan/7916117/working/building/REAL250005035495 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035495 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035495/0 /scratch/stefan/7916117/working/building/REAL250005035495 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/46 `/scratch/stefan/7916117/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035495.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035495 none CCN(CC)C(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 155, 151, 155, 173, 120, 151, 109, 108, 48, 48, 48, 22, 8, 1, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 180, 173, 173, 173, 173, 173, 117, 118, 114, 114, 108, 108, 48, 23, 22, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 908 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035495 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035495 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035495/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035495 Building REAL250005035496 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035496' /scratch/stefan/7916117/working/building/REAL250005035496 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035496 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035496/0 /scratch/stefan/7916117/working/building/REAL250005035496 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/47 `/scratch/stefan/7916117/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCCCC1) `REAL250005035496.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035496 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 59, 89, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 1, 1, 11, 59, 59, 89, 89, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 143 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 454 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: REAL250005035496 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 96, 143, 143, 143, 143, 143, 143, 96, 24, 25, 8, 8, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143] 143 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 462 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035496 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035496 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035496/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035496 Building REAL250005035497 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035497' /scratch/stefan/7916117/working/building/REAL250005035497 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035497 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035497/0 /scratch/stefan/7916117/working/building/REAL250005035497 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/48 `/scratch/stefan/7916117/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)CC1CCCC1)NCCC1=NC(=O)O[N-]1) `REAL250005035497.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035497 none O=C(CNC(=O)CC1CCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [35, 35, 35, 64, 76, 76, 76, 189, 201, 201, 201, 201, 16, 8, 1, 1, 1, 1, 1, 1, 1, 64, 64, 76, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 35, 16, 16, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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: REAL250005035497 none O=C(CNC(=O)CC1CCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [90, 81, 22, 22, 5, 22, 1, 1, 1, 1, 1, 1, 86, 86, 130, 130, 201, 201, 201, 201, 201, 81, 81, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 90, 130, 130, 130, 130] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39]) total number of confs: 692 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035497 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035497 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035497/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035497 Building REAL250005035498 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035498' /scratch/stefan/7916117/working/building/REAL250005035498 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035498 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035498/0 /scratch/stefan/7916117/working/building/REAL250005035498 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/49 `/scratch/stefan/7916117/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1F) `REAL250005035498.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035498 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [12, 1, 12, 13, 72, 102, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 13, 72, 72, 102, 102, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 584 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035498 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 97, 201, 201, 201, 201, 201, 201, 201, 97, 24, 24, 8, 8, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035498 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035498 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035498/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035498 Building REAL250005035499 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035499' /scratch/stefan/7916117/working/building/REAL250005035499 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035499 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035499/0 /scratch/stefan/7916117/working/building/REAL250005035499 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/50 `/scratch/stefan/7916117/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOCC1) `REAL250005035499.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035499 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 61, 61, 61, 22, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 105, 105, 61, 23, 23, 8, 8, 105, 105, 105, 105, 105, 105, 105, 105] 105 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 387 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035499 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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 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, 4, 4, 4, 21, 37, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 2, 2, 2, 4, 21, 21, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1] 105 rigid atoms, others: [0, 1, 2, 33, 32, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035499 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035499 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035499/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035499 Building REAL250005035500 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035500' /scratch/stefan/7916117/working/building/REAL250005035500 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035500 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035500/0 /scratch/stefan/7916117/working/building/REAL250005035500 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/51 `/scratch/stefan/7916117/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=CC(F)=C1F)NCCC1=NC(=O)O[N-]1) `REAL250005035500.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035500 none O=C(CCC1=CC=CC(F)=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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, 41, 41, 149, 183, 201, 201, 201, 201, 201, 201, 201, 15, 7, 1, 1, 1, 1, 1, 1, 1, 149, 149, 183, 183, 201, 201, 201, 41, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035500 none O=C(CCC1=CC=CC(F)=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [31, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 102, 102, 201, 201, 201, 201, 201, 9, 9, 5, 5, 1, 1, 1, 31, 102, 102, 102, 102] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 1, 2, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 559 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035500 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035500 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035500/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035500 Building REAL250005035501 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035501' /scratch/stefan/7916117/working/building/REAL250005035501 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035501 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035501/0 /scratch/stefan/7916117/working/building/REAL250005035501 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/52 `/scratch/stefan/7916117/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC(CC(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035501.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035501 none CC1CCCC(CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 155, 54, 54, 54, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 155, 54, 17, 17, 8, 8, 201, 201] 201 rigid atoms, others: [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, 36, 37, 38]) total number of confs: 755 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035501 none CC1CCCC(CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 28, 28, 28, 94, 96, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 28, 94, 94, 96, 96, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 18, 22, 23, 24, 25, 26, 27, 28, 29, 37] set([32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 30, 31]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035501 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035501 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035501/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035501 Building REAL250005035502 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035502' /scratch/stefan/7916117/working/building/REAL250005035502 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035502 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035502/0 /scratch/stefan/7916117/working/building/REAL250005035502 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/53 `/scratch/stefan/7916117/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(O)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035502.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035502 none CC(C)C1=CC=C(O)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 191, 201, 191, 144, 191, 191, 191, 87, 87, 87, 24, 8, 1, 1, 1, 1, 1, 1, 1, 191, 201, 201, 201, 201, 201, 201, 201, 191, 191, 382, 86, 24, 25, 8, 8, 191] 402 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1075 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035502 none CC(C)C1=CC=C(O)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 65, 191, 191, 191, 191, 191, 1, 5, 5, 5, 4, 4, 4, 4, 1, 1, 2, 9, 49, 49, 65, 65, 1] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 20, 36, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035502 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035502 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035502/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035502 Building REAL250005035503 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035503' /scratch/stefan/7916117/working/building/REAL250005035503 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035503 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035503/0 /scratch/stefan/7916117/working/building/REAL250005035503 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/54 `/scratch/stefan/7916117/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)F)C=C1) `REAL250005035503.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035503 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 23, 43, 146, 146, 146, 146, 146, 1, 1, 1, 1, 1, 12, 12, 1, 1, 4, 23, 23, 43, 43, 1, 1, 12, 1, 1] 197 rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 19, 25, 26, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 20, 21, 22, 23, 24, 27]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035503 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 24, 8, 1, 1, 1, 1, 1, 1, 1, 92, 146, 146, 92, 92, 197, 197, 146, 146, 92, 24, 24, 8, 8, 146, 146, 197, 146, 146] 197 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 999 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035503 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035503 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035503/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035503 Building REAL250005035504 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035504' /scratch/stefan/7916117/working/building/REAL250005035504 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035504 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035504/0 /scratch/stefan/7916117/working/building/REAL250005035504 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/55 `/scratch/stefan/7916117/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC=C21) `REAL250005035504.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035504 none CN1C=CC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 193, 193, 83, 83, 83, 23, 8, 1, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 193, 193, 193, 193, 83, 24, 24, 8, 8, 193, 193, 193] 193 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL250005035504 none CN1C=CC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 63, 91, 193, 193, 193, 193, 193, 1, 1, 1, 1, 2, 2, 2, 1, 1, 11, 63, 63, 91, 91, 1, 1, 1] 193 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 17, 18, 19, 20, 24, 25, 33, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035504 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035504 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035504/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035504 Building REAL250005035505 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035505' /scratch/stefan/7916117/working/building/REAL250005035505 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035505 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035505/0 /scratch/stefan/7916117/working/building/REAL250005035505 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/56 `/scratch/stefan/7916117/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1) `REAL250005035505.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035505 none CC(C)(C)C1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 125, 201, 201, 125, 125, 85, 85, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 24, 24, 8, 8, 125] 201 rigid atoms, others: [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]) 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: REAL250005035505 none CC(C)(C)C1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 10, 10, 10, 45, 63, 125, 125, 125, 125, 125, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 45, 45, 63, 63, 1] 201 rigid atoms, others: [1, 34, 4, 5, 6, 7, 18, 19] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035505 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035505 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035505/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035505 Building REAL250005035506 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035506' /scratch/stefan/7916117/working/building/REAL250005035506 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035506 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035506/0 /scratch/stefan/7916117/working/building/REAL250005035506 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/57 `/scratch/stefan/7916117/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1) `REAL250005035506.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035506 none CC(C)C1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 151, 201, 151, 151, 91, 91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 152, 152, 201, 201, 201, 201, 201, 201, 201, 90, 24, 24, 8, 8, 152] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 673 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035506 none CC(C)C1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 1, 1, 1, 1, 6, 6, 6, 32, 41, 151, 151, 151, 151, 151, 1, 1, 13, 13, 13, 12, 13, 13, 13, 6, 32, 32, 41, 41, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035506 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035506 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035506/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035506 Building REAL250005035507 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035507' /scratch/stefan/7916117/working/building/REAL250005035507 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035507 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035507/0 /scratch/stefan/7916117/working/building/REAL250005035507 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/58 `/scratch/stefan/7916117/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035507.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035507 none N#CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 147, 56, 56, 56, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 147, 147, 56, 19, 19, 8, 8, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 701 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035507 none N#CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 63, 78, 201, 201, 201, 201, 201, 1, 1, 1, 1, 5, 5, 11, 63, 63, 78, 78, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 500 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035507 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035507 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035507/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035507 Building REAL250005035508 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035508' /scratch/stefan/7916117/working/building/REAL250005035508 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035508 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035508/0 /scratch/stefan/7916117/working/building/REAL250005035508 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/59 `/scratch/stefan/7916117/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=CNN=C2C(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035508.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035508 none CC1=CC2=CNN=C2C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [163, 162, 163, 163, 163, 163, 163, 163, 82, 82, 82, 23, 8, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 163, 163, 163, 82, 24, 24, 8, 8, 163] 163 rigid atoms, others: [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]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035508 none CC1=CC2=CNN=C2C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 58, 79, 163, 163, 163, 163, 163, 1, 2, 2, 2, 1, 1, 1, 12, 58, 58, 79, 79, 1] 163 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 32, 24, 25, 26] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035508 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035508 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035508/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035508 Building REAL250005035509 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035509' /scratch/stefan/7916117/working/building/REAL250005035509 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035509 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035509/0 /scratch/stefan/7916117/working/building/REAL250005035509 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/60 `/scratch/stefan/7916117/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CN1CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035509.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035509 none CC1=NC=CN1CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 115, 81, 93, 27, 27, 27, 11, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 113, 113, 115, 115, 93, 93, 27, 11, 11, 5, 5] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 857 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035509 none CC1=NC=CN1CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 6, 8, 15, 41, 41, 41, 109, 109, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 6, 6, 8, 8, 15, 15, 41, 109, 109, 109, 109] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 617 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035509 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035509/1 /scratch/stefan/7916117/working/building/REAL250005035509 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/61 `/scratch/stefan/7916117/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=[NH+]C=CN1CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035509.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035509 none CC1=[NH+]C=CN1CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 188, 188, 188, 137, 102, 135, 68, 68, 68, 17, 8, 1, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 130, 127, 137, 137, 135, 135, 68, 17, 17, 8, 8] 188 rigid atoms, others: [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]) total number of confs: 842 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035509 none CC1=[NH+]C=CN1CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 10, 15, 37, 37, 37, 88, 88, 188, 188, 188, 188, 188, 2, 2, 2, 1, 1, 6, 6, 10, 10, 15, 15, 37, 88, 88, 88, 88] 188 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035509 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035509 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035509/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035509/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035509 Building REAL250005035510 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035510' /scratch/stefan/7916117/working/building/REAL250005035510 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035510 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035510/0 /scratch/stefan/7916117/working/building/REAL250005035510 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/62 `/scratch/stefan/7916117/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1F) `REAL250005035510.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035510 none CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 16, 62, 62, 62, 126, 126, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 16, 16, 62, 126, 126, 126, 126, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 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: REAL250005035510 none CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 128, 43, 43, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 160, 201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 134, 134, 43, 8, 8, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035510 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035510 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035510/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035510 Building REAL250005035511 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035511' /scratch/stefan/7916117/working/building/REAL250005035511 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035511 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035511/0 /scratch/stefan/7916117/working/building/REAL250005035511 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/63 `/scratch/stefan/7916117/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005035511.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035511 none CC(=CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 28, 28, 28, 103, 124, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 28, 103, 103, 124, 124, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 612 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035511 none CC(=CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 128, 66, 66, 66, 23, 8, 1, 1, 1, 1, 1, 1, 1, 135, 201, 201, 201, 201, 201, 135, 135, 135, 135, 65, 23, 23, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035511 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035511 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035511/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035511 Building REAL250005035512 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035512' /scratch/stefan/7916117/working/building/REAL250005035512 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035512 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035512/0 /scratch/stefan/7916117/working/building/REAL250005035512 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/64 `/scratch/stefan/7916117/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C(Cl)C=C1) `REAL250005035512.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035512 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 31, 31, 88, 93, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 1, 31, 88, 88, 93, 93, 1, 1, 1, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24]) total number of confs: 532 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035512 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 19, 8, 1, 1, 1, 1, 1, 1, 1, 69, 137, 137, 201, 201, 137, 139, 201, 201, 69, 19, 19, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035512 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035512 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035512/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035512 Building REAL250005035513 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035513' /scratch/stefan/7916117/working/building/REAL250005035513 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035513 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035513/0 /scratch/stefan/7916117/working/building/REAL250005035513 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/65 `/scratch/stefan/7916117/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CC(Cl)=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035513.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035513 none O=C(CC1=CC=CC(Cl)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [51, 51, 51, 115, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 115, 115, 201, 201, 201, 201, 51, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 612 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035513 none O=C(CC1=CC=CC(Cl)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 76, 82, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 17, 76, 76, 82, 82] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 495 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035513 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035513 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035513/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035513 Building REAL250005035514 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035514' /scratch/stefan/7916117/working/building/REAL250005035514 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035514 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035514/0 /scratch/stefan/7916117/working/building/REAL250005035514 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/66 `/scratch/stefan/7916117/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(O)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035514.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035514 none CCC1=CC=C(O)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 121, 121, 111, 121, 121, 121, 70, 70, 70, 22, 8, 1, 1, 1, 1, 1, 1, 1, 121, 201, 201, 201, 201, 201, 121, 121, 242, 69, 22, 23, 8, 8, 121] 402 rigid atoms, others: [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]) total number of confs: 1075 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035514 none CCC1=CC=C(O)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 35, 53, 121, 121, 121, 121, 121, 1, 6, 6, 6, 6, 6, 1, 1, 2, 8, 35, 35, 53, 53, 1] 402 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 33, 19, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035514 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035514 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035514/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035514 Building REAL250005035515 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035515' /scratch/stefan/7916117/working/building/REAL250005035515 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035515 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035515/0 /scratch/stefan/7916117/working/building/REAL250005035515 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/67 `/scratch/stefan/7916117/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1C(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035515.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035515 none CC1=NOC(C)=C1C(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 153, 75, 153, 75, 75, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 153, 153, 153, 153, 75, 20, 20, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 708 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035515 none CC1=NOC(C)=C1C(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 15, 15, 72, 90, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 15, 72, 72, 90, 90] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 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: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035515 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035515 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035515/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035515 Building REAL250005035516 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035516' /scratch/stefan/7916117/working/building/REAL250005035516 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035516 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035516/0 /scratch/stefan/7916117/working/building/REAL250005035516 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/68 `/scratch/stefan/7916117/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035516.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035516 none CC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 100, 201, 201, 100, 45, 45, 45, 17, 8, 1, 1, 1, 1, 1, 1, 1, 182, 201, 201, 201, 100, 201, 201, 100, 100, 45, 17, 17, 8, 8, 201] 201 rigid atoms, others: [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]) total number of confs: 893 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035516 none CC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 6, 17, 17, 17, 73, 81, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 6, 6, 17, 73, 73, 81, 81, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 18, 22, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035516 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035516 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035516/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035516 Building REAL250005035517 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035517' /scratch/stefan/7916117/working/building/REAL250005035517 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035517 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035517/0 /scratch/stefan/7916117/working/building/REAL250005035517 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/69 `/scratch/stefan/7916117/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CC=C1O)NCCC1=NC(=O)O[N-]1) `REAL250005035517.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035517 none O=C(CC1=CC=CC=C1O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 143, 201, 201, 177, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 201, 402, 41, 17, 17, 8, 8] 402 rigid atoms, others: [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]) total number of confs: 1168 number of broken/clashed sets: 198 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035517 none O=C(CC1=CC=CC=C1O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 101, 107, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 2, 35, 101, 101, 107, 107] 402 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30]) total number of confs: 578 number of broken/clashed sets: 198 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035517 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035517 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035517/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035517 Building REAL250005035518 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035518' /scratch/stefan/7916117/working/building/REAL250005035518 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035518 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035518/0 /scratch/stefan/7916117/working/building/REAL250005035518 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/70 `/scratch/stefan/7916117/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)[NH+]1C(C)CCC1C) `REAL250005035518.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035518 none CC(C(=O)NCCC1=NC(=O)O[N-]1)[NH+]1C(C)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.4', 'H', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 4, 4, 4, 15, 20, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 4, 15, 15, 20, 20, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2] 49 rigid atoms, others: [1, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 39, 40, 41]) total number of confs: 142 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: REAL250005035518 none CC(C(=O)NCCC1=NC(=O)O[N-]1)[NH+]1C(C)CCC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.4', 'H', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 39, 39, 39, 17, 8, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 39, 17, 17, 8, 8, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 49 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 206 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035518 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035518 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035518/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035518 Building REAL250005035519 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035519' /scratch/stefan/7916117/working/building/REAL250005035519 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035519 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035519/0 /scratch/stefan/7916117/working/building/REAL250005035519 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/71 `/scratch/stefan/7916117/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005035519.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035519 none CCSC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 107, 107, 107, 107, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 107, 107, 201, 201, 201, 201, 201, 107, 107, 49, 17, 17, 8, 8, 107] 201 rigid atoms, others: [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]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035519 none CCSC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 25, 107, 107, 107, 107, 107, 1, 1, 35, 35, 35, 35, 35, 1, 1, 5, 23, 23, 25, 25, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 18, 19, 25, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035519 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035519 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035519/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035519 Building REAL250005035520 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035520' /scratch/stefan/7916117/working/building/REAL250005035520 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035520 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035520/0 /scratch/stefan/7916117/working/building/REAL250005035520 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/72 `/scratch/stefan/7916117/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCOC2=CC=CC=C21) `REAL250005035520.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035520 none O=C(NCCC1=NC(=O)O[N-]1)C1CCOC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 48, 65, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 48, 48, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1] 147 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 387 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: REAL250005035520 none O=C(NCCC1=NC(=O)O[N-]1)C1CCOC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 81, 147, 147, 147, 147, 147, 147, 147, 147, 147, 81, 24, 24, 8, 8, 147, 147, 147, 147, 147, 147, 147, 147, 147] 147 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 469 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035520 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035520 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035520/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035520 Building REAL250005035521 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035521' /scratch/stefan/7916117/working/building/REAL250005035521 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035521 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035521/0 /scratch/stefan/7916117/working/building/REAL250005035521 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/73 `/scratch/stefan/7916117/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035521.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035521 none CCC1=CC=C(C(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 104, 201, 201, 104, 51, 104, 51, 51, 18, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 104, 104, 104, 51, 18, 18, 8, 8, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035521 none CCC1=CC=C(C(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 98, 108, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 26, 98, 98, 108, 108, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37] set([32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 582 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035521 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035521 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035521/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035521 Building REAL250005035522 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035522' /scratch/stefan/7916117/working/building/REAL250005035522 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035522 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035522/0 /scratch/stefan/7916117/working/building/REAL250005035522 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/74 `/scratch/stefan/7916117/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)NCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035522.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035522 none CC(C)CCC(=O)NCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 199, 201, 196, 96, 96, 101, 79, 36, 36, 36, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 101, 79, 79, 35, 9, 8, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 848 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035522 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035522 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035522/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035522 Building REAL250005035523 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035523' /scratch/stefan/7916117/working/building/REAL250005035523 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035523 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035523/0 /scratch/stefan/7916117/working/building/REAL250005035523 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/75 `/scratch/stefan/7916117/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC(C(=O)NCCC1=NC(=O)O[N-]1)C(C)C) `REAL250005035523.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035523 none CCSC(C(=O)NCCC1=NC(=O)O[N-]1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 14, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 185, 147, 55, 55, 55, 8, 8, 1, 1, 1, 1, 1, 1, 1, 144, 180, 177, 198, 198, 198, 198, 198, 147, 54, 8, 9, 8, 8, 180, 180, 180, 180, 180, 180, 180] 201 rigid atoms, others: [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, 33, 34, 35]) total number of confs: 847 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035523 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035523 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035523/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035523 Building REAL250005035524 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035524' /scratch/stefan/7916117/working/building/REAL250005035524 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035524 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035524/0 /scratch/stefan/7916117/working/building/REAL250005035524 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/76 `/scratch/stefan/7916117/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(CC(=O)NCCC2=NC(=O)O[N-]2)CC(C)(C)C1) `REAL250005035524.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035524 none CC1CC(CC(=O)NCCC2=NC(=O)O[N-]2)CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 162, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 49, 17, 17, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 763 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: REAL250005035524 none CC1CC(CC(=O)NCCC2=NC(=O)O[N-]2)CC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 101, 106, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 8, 28, 101, 101, 106, 106, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 43, 44, 16, 17, 18, 35, 20, 24, 25, 26, 27, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 575 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035524 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035524 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035524/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035524 Building REAL250005035525 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035525' /scratch/stefan/7916117/working/building/REAL250005035525 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035525 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035525/0 /scratch/stefan/7916117/working/building/REAL250005035525 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/77 `/scratch/stefan/7916117/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035525.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035525 none CC(C)CC(C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 182, 200, 64, 64, 64, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 182, 182, 64, 19, 19, 8, 8] 201 rigid atoms, others: [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, 36, 37]) total number of confs: 824 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035525 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035525 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035525/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035525 Building REAL250005035526 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035526' /scratch/stefan/7916117/working/building/REAL250005035526 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035526 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035526/0 /scratch/stefan/7916117/working/building/REAL250005035526 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/78 `/scratch/stefan/7916117/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCC(C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035526.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035526 none CCCCCCC(C)CC(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 119, 164, 35, 35, 35, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 119, 119, 35, 15, 15, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 930 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035526 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035526 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035526/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035526 Building REAL250005035527 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035527' /scratch/stefan/7916117/working/building/REAL250005035527 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035527 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035527/0 /scratch/stefan/7916117/working/building/REAL250005035527 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/79 `/scratch/stefan/7916117/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035527.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035527 none CC1=CC=C(F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 92, 92, 92, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 92, 24, 24, 8, 8, 201] 201 rigid atoms, others: [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]) total number of confs: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035527 none CC1=CC=C(F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 65, 98, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 13, 65, 65, 98, 98, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 22, 23, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 588 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035527 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035527 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035527/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035527 Building REAL250005035528 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035528' /scratch/stefan/7916117/working/building/REAL250005035528 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035528 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035528/0 /scratch/stefan/7916117/working/building/REAL250005035528 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/80 `/scratch/stefan/7916117/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1CCCC1=O)NCCC1=NC(=O)O[N-]1) `REAL250005035528.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035528 none O=C(CCN1CCCC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [52, 52, 52, 159, 177, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 159, 159, 178, 178, 201, 201, 201, 201, 201, 201, 52, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035528 none O=C(CCN1CCCC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 14, 9, 1, 1, 1, 1, 1, 1, 1, 48, 48, 116, 128, 201, 201, 201, 201, 201, 14, 14, 9, 9, 1, 1, 1, 1, 1, 1, 48, 121, 121, 126, 127] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 33, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 643 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035528 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035528 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035528/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035528 Building REAL250005035529 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035529' /scratch/stefan/7916117/working/building/REAL250005035529 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035529 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035529/0 /scratch/stefan/7916117/working/building/REAL250005035529 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/81 `/scratch/stefan/7916117/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C)C(CC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035529.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035529 none CC1=CC=C(C)C(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 150, 47, 47, 47, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 150, 150, 47, 19, 19, 8, 8, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 655 number of broken/clashed sets: 148 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035529 none CC1=CC=C(C)C(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 27, 27, 27, 92, 96, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 2, 2, 2, 4, 4, 27, 92, 92, 96, 96, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 23, 24, 35] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 525 number of broken/clashed sets: 148 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035529 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035529 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035529/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035529 Building REAL250005035530 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035530' /scratch/stefan/7916117/working/building/REAL250005035530 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035530 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035530/0 /scratch/stefan/7916117/working/building/REAL250005035530 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/82 `/scratch/stefan/7916117/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C(F)F) `REAL250005035530.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035530 none CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [198, 198, 198, 198, 81, 81, 81, 20, 8, 1, 1, 1, 1, 1, 1, 1, 198, 198, 201, 201, 198, 198, 198, 198, 80, 20, 20, 8, 8, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL250005035530 none CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 10, 10, 11, 53, 73, 198, 198, 198, 198, 198, 1, 1, 7, 7, 2, 2, 2, 1, 11, 53, 53, 73, 73, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 500 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035530 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035530 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035530/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035530 Building REAL250005035531 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035531' /scratch/stefan/7916117/working/building/REAL250005035531 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035531 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035531/0 /scratch/stefan/7916117/working/building/REAL250005035531 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/83 `/scratch/stefan/7916117/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005035531.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035531 none CNC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 170, 201, 63, 63, 63, 16, 8, 1, 1, 1, 1, 1, 1, 1, 170, 170, 201, 201, 201, 201, 63, 16, 16, 8, 8, 170, 170, 170, 170] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 612 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: REAL250005035531 none CNC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 5, 1, 1, 7, 7, 7, 42, 53, 170, 170, 170, 170, 170, 1, 1, 5, 5, 5, 5, 7, 42, 42, 53, 53, 1, 1, 1, 1] 201 rigid atoms, others: [2, 4, 5, 16, 17, 27, 28, 29, 30] set([0, 1, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 375 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035531 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035531 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035531/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035531 Building REAL250005035532 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035532' /scratch/stefan/7916117/working/building/REAL250005035532 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035532 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035532/0 /scratch/stefan/7916117/working/building/REAL250005035532 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/84 `/scratch/stefan/7916117/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035532.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035532 none CCNC(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 134, 134, 134, 134, 100, 95, 22, 22, 22, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 134, 122, 122, 124, 124, 96, 96, 22, 19, 19, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1091 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035532 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035532 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035532/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035532 Building REAL250005035533 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035533' /scratch/stefan/7916117/working/building/REAL250005035533 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035533 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035533/0 /scratch/stefan/7916117/working/building/REAL250005035533 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/85 `/scratch/stefan/7916117/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035533.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035533 none CCCNC(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 151, 92, 92, 80, 92, 63, 65, 19, 19, 19, 13, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 151, 151, 92, 75, 76, 72, 72, 65, 65, 19, 13, 13, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1049 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035533 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035533 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035533/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035533 Building REAL250005035534 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035534' /scratch/stefan/7916117/working/building/REAL250005035534 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035534 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035534/0 /scratch/stefan/7916117/working/building/REAL250005035534 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/86 `/scratch/stefan/7916117/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035534.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035534 none CC(C)NC(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 187, 201, 138, 133, 33, 33, 33, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 197, 170, 170, 174, 174, 135, 135, 33, 21, 21, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1009 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035534 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035534 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035534/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035534 Building REAL250005035535 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035535' /scratch/stefan/7916117/working/building/REAL250005035535 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035535 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035535/0 /scratch/stefan/7916117/working/building/REAL250005035535 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/87 `/scratch/stefan/7916117/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[NH+](CCC)CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035535.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035535 none CCC[NH+](CCC)CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [64, 46, 43, 27, 43, 43, 46, 64, 23, 27, 23, 23, 23, 13, 7, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 46, 46, 46, 46, 64, 64, 64, 64, 64, 27, 27, 27, 27, 27, 27, 23, 13, 13, 7, 7] 69 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 478 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035535 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035535 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035535/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035535 Building REAL250005035536 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035536' /scratch/stefan/7916117/working/building/REAL250005035536 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035536 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035536/0 /scratch/stefan/7916117/working/building/REAL250005035536 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/88 `/scratch/stefan/7916117/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035536.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035536 none CC(C)OC1=CC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 179, 179, 179, 101, 179, 179, 73, 73, 73, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 179, 179, 179, 179, 72, 25, 25, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 746 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: REAL250005035536 none CC(C)OC1=CC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 34, 44, 179, 179, 179, 179, 179, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 12, 34, 34, 44, 44] 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]) total number of confs: 393 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035536 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035536 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035536/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035536 Building REAL250005035537 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035537' /scratch/stefan/7916117/working/building/REAL250005035537 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035537 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035537/0 /scratch/stefan/7916117/working/building/REAL250005035537 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/89 `/scratch/stefan/7916117/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1O) `REAL250005035537.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035537 none COC1=CC(C)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 148, 144, 148, 148, 148, 148, 77, 77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 148, 148, 201, 201, 201, 148, 148, 148, 148, 148, 77, 25, 25, 8, 8, 296] 402 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 789 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035537 none COC1=CC(C)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 1, 1, 1, 7, 7, 7, 41, 60, 148, 148, 148, 148, 148, 1, 1, 3, 3, 3, 1, 2, 2, 2, 1, 7, 41, 41, 60, 60, 2] 402 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 24, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035537 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035537 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035537/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035537 Building REAL250005035538 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035538' /scratch/stefan/7916117/working/building/REAL250005035538 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035538 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035538/0 /scratch/stefan/7916117/working/building/REAL250005035538 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/90 `/scratch/stefan/7916117/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1) `REAL250005035538.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035538 none CNC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 190, 201, 69, 69, 69, 17, 8, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 201, 201, 201, 201, 69, 17, 17, 8, 8, 190, 190, 190, 190, 190, 190] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 592 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: REAL250005035538 none CNC(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 5, 1, 5, 1, 1, 7, 7, 7, 40, 52, 190, 190, 190, 190, 190, 1, 1, 1, 5, 5, 5, 5, 7, 40, 40, 52, 52, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 4, 5, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 401 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035538 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035538 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035538/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035538 Building REAL250005035539 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035539' /scratch/stefan/7916117/working/building/REAL250005035539 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035539 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035539/0 /scratch/stefan/7916117/working/building/REAL250005035539 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/91 `/scratch/stefan/7916117/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC([N+](=O)[O-])=C1) `REAL250005035539.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035539 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 47, 77, 197, 197, 197, 197, 197, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 47, 47, 77, 77, 1, 1, 1] 197 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 509 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035539 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [76, 75, 20, 8, 1, 1, 1, 1, 1, 1, 1, 76, 197, 197, 197, 196, 197, 197, 197, 197, 197, 75, 20, 20, 8, 8, 197, 197, 197] 197 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035539 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035539 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035539/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035539 Building REAL250005035540 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035540' /scratch/stefan/7916117/working/building/REAL250005035540 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035540 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035540/0 /scratch/stefan/7916117/working/building/REAL250005035540 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/92 `/scratch/stefan/7916117/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=C1) `REAL250005035540.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035540 none COC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 171, 171, 68, 68, 68, 22, 8, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 201, 201, 201, 68, 22, 22, 8, 8, 171, 171] 201 rigid atoms, others: [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]) total number of confs: 427 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035540 none COC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 12, 12, 12, 54, 73, 171, 171, 171, 171, 171, 1, 1, 1, 4, 4, 4, 12, 54, 54, 73, 73, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 15, 16, 17, 26, 27] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035540 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035540 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035540/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035540 Building REAL250005035541 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035541' /scratch/stefan/7916117/working/building/REAL250005035541 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035541 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035541/0 /scratch/stefan/7916117/working/building/REAL250005035541 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/93 `/scratch/stefan/7916117/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=N1) `REAL250005035541.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035541 none CNC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 8, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 142, 142, 142, 70, 70, 70, 19, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 201, 201, 201, 201, 142, 70, 19, 19, 8, 8, 142] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 560 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035541 none CNC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 8, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [6, 1, 1, 1, 1, 1, 5, 5, 5, 27, 37, 142, 142, 142, 142, 142, 1, 1, 1, 1, 6, 6, 6, 6, 1, 5, 27, 27, 37, 37, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 24, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035541 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035541 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035541/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035541 Building REAL250005035542 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035542' /scratch/stefan/7916117/working/building/REAL250005035542 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035542 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035542/0 /scratch/stefan/7916117/working/building/REAL250005035542 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/94 `/scratch/stefan/7916117/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(O)=C1) `REAL250005035542.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035542 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(O)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 4, 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: [7, 1, 7, 7, 34, 59, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 1, 7, 34, 34, 59, 59, 1, 1, 2, 1] 242 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 25]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035542 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(O)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 4, 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: [55, 55, 20, 8, 1, 1, 1, 1, 1, 1, 1, 55, 121, 121, 121, 121, 121, 121, 55, 20, 20, 8, 8, 121, 121, 242, 121] 242 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035542 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035542/1 /scratch/stefan/7916117/working/building/REAL250005035542 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/95 `/scratch/stefan/7916117/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC([O-])=C1) `REAL250005035542.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035542 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC([O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 3, 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: [6, 1, 6, 6, 29, 38, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 6, 29, 29, 38, 38, 1, 1, 1] 76 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 215 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035542 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC([O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 24, 8, 1, 1, 1, 1, 1, 1, 1, 55, 76, 76, 76, 76, 76, 76, 54, 24, 24, 8, 8, 76, 76, 76] 76 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035542 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035542 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035542/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035542/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035542 Building REAL250005035543 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035543' /scratch/stefan/7916117/working/building/REAL250005035543 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035543 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035543/0 /scratch/stefan/7916117/working/building/REAL250005035543 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/96 `/scratch/stefan/7916117/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=CN=C2C=C1) `REAL250005035543.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035543 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 49, 79, 146, 146, 146, 146, 146, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 49, 49, 79, 79, 1, 1, 1, 1, 1] 146 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 446 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035543 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 22, 8, 1, 1, 1, 1, 1, 1, 1, 64, 146, 146, 146, 146, 146, 146, 146, 146, 64, 22, 22, 8, 8, 146, 146, 146, 146, 146] 146 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035543 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035543 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035543/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035543 Building REAL250005035544 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035544' /scratch/stefan/7916117/working/building/REAL250005035544 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035544 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035544/0 /scratch/stefan/7916117/working/building/REAL250005035544 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/97 `/scratch/stefan/7916117/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035544.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035544 none CC1=CC=C(C(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 187, 201, 201, 176, 70, 176, 70, 70, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 176, 70, 24, 24, 8, 8, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035544 none CC1=CC=C(C(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 8, 8, 24, 24, 24, 86, 98, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 8, 9, 9, 9, 24, 86, 86, 98, 98, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 34, 18, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 566 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035544 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035544 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035544/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035544 Building REAL250005035545 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035545' /scratch/stefan/7916117/working/building/REAL250005035545 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035545 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035545/0 /scratch/stefan/7916117/working/building/REAL250005035545 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/98 `/scratch/stefan/7916117/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005035545.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035545 none CNC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 144, 164, 144, 144, 144, 69, 70, 70, 22, 8, 1, 1, 1, 1, 1, 1, 1, 144, 144, 164, 164, 164, 164, 144, 144, 69, 22, 22, 8, 8, 144] 164 rigid atoms, others: [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]) total number of confs: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035545 none CNC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 9, 1, 1, 1, 1, 1, 7, 7, 7, 35, 61, 144, 144, 144, 144, 144, 1, 1, 10, 10, 10, 10, 1, 1, 7, 35, 35, 61, 61, 1] 164 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 19, 20, 25, 26] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035545 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035545 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035545/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035545 Building REAL250005035546 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035546' /scratch/stefan/7916117/working/building/REAL250005035546 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035546 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035546/0 /scratch/stefan/7916117/working/building/REAL250005035546 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/99 `/scratch/stefan/7916117/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL250005035546.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035546 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 55, 55, 55, 21, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 130, 55, 21, 21, 8, 8, 130] 130 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035546 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 41, 66, 130, 130, 130, 130, 130, 1, 1, 1, 2, 2, 2, 1, 1, 7, 41, 41, 66, 66, 1] 130 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 22, 23, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035546 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035546 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035546/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035546 Building REAL250005035547 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035547' /scratch/stefan/7916117/working/building/REAL250005035547 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035547 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035547/0 /scratch/stefan/7916117/working/building/REAL250005035547 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/100 `/scratch/stefan/7916117/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(CCOC2)S1) `REAL250005035547.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035547 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(CCOC2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 12, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 65, 90, 157, 156, 157, 156, 156, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 65, 65, 91, 91, 1, 1, 1, 1, 1, 1, 1] 157 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 489 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035547 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(CCOC2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 12, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 23, 8, 1, 1, 1, 1, 1, 1, 1, 84, 157, 157, 157, 156, 157, 157, 157, 156, 83, 23, 23, 8, 8, 157, 156, 156, 157, 157, 157, 157] 157 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035547 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035547 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035547/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035547 Building REAL250005035548 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035548' /scratch/stefan/7916117/working/building/REAL250005035548 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035548 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035548/0 /scratch/stefan/7916117/working/building/REAL250005035548 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/101 `/scratch/stefan/7916117/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CC2)C=CS1) `REAL250005035548.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035548 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CC2)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 52, 69, 175, 175, 175, 175, 175, 1, 1, 1, 7, 7, 1, 1, 1, 12, 52, 52, 69, 69, 7, 7, 7, 7, 7, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 16, 17, 18, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005035548 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CC2)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 76, 23, 8, 1, 1, 1, 1, 1, 1, 1, 76, 175, 175, 201, 201, 175, 175, 175, 76, 23, 23, 8, 8, 201, 201, 201, 201, 201, 175, 175] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 494 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035548 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CC2)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 28, 28, 87, 104, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 7, 7, 7, 28, 87, 87, 104, 104, 1, 1, 1, 1, 1, 7, 7] 201 rigid atoms, others: [12, 13, 14, 15, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30]) total number of confs: 569 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035548 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035548 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035548/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035548 Building REAL250005035549 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035549' /scratch/stefan/7916117/working/building/REAL250005035549 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035549 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035549/0 /scratch/stefan/7916117/working/building/REAL250005035549 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/102 `/scratch/stefan/7916117/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NCCC1=NC(=O)O[N-]1)C(=O)C1CC1) `REAL250005035549.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035549 none CN(CC(=O)NCCC1=NC(=O)O[N-]1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 7, 19, 30, 29, 30, 87, 101, 201, 201, 201, 201, 201, 1, 5, 1, 1, 1, 7, 7, 7, 19, 19, 30, 87, 87, 101, 101, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 14, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005035549 none CN(CC(=O)NCCC1=NC(=O)O[N-]1)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 105, 61, 61, 61, 19, 8, 1, 1, 1, 1, 1, 1, 1, 120, 141, 140, 201, 201, 123, 123, 123, 105, 105, 61, 19, 19, 8, 8, 200, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 819 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035549 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035549 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035549/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035549 Building REAL250005035550 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035550' /scratch/stefan/7916117/working/building/REAL250005035550 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035550 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035550/0 /scratch/stefan/7916117/working/building/REAL250005035550 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/103 `/scratch/stefan/7916117/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC[N@H+](C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035550.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035550 none CCCCCC[N@H+](C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 171, 151, 136, 103, 87, 103, 101, 48, 48, 48, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 196, 171, 171, 151, 151, 136, 136, 103, 103, 103, 87, 87, 48, 17, 17, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 977 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035550 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035550/1 /scratch/stefan/7916117/working/building/REAL250005035550 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/104 `/scratch/stefan/7916117/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC[N@@H+](C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035550.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005035550 none CCCCCC[N@@H+](C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 170, 149, 134, 103, 86, 103, 102, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 196, 170, 170, 149, 149, 134, 134, 103, 103, 103, 86, 86, 49, 17, 17, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 968 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035550 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035550 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035550/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035550/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035550 Building REAL250005035551 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035551' /scratch/stefan/7916117/working/building/REAL250005035551 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035551 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035551/0 /scratch/stefan/7916117/working/building/REAL250005035551 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/105 `/scratch/stefan/7916117/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC2=CN=CN21) `REAL250005035551.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035551 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC2=CN=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [12, 1, 12, 12, 71, 96, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 12, 71, 71, 96, 96, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 545 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035551 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC2=CN=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [97, 97, 20, 8, 1, 1, 1, 1, 1, 1, 1, 97, 201, 201, 201, 201, 201, 201, 201, 97, 20, 20, 8, 8, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 443 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035551 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035551 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035551/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035551 Building REAL250005035552 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035552' /scratch/stefan/7916117/working/building/REAL250005035552 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035552 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035552/0 /scratch/stefan/7916117/working/building/REAL250005035552 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/106 `/scratch/stefan/7916117/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCC(=O)NC1=O)NCCC1=NC(=O)O[N-]1) `REAL250005035552.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035552 none O=C(CN1CCC(=O)NC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 1, 11, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [57, 57, 57, 190, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 190, 190, 201, 201, 201, 201, 201, 57, 19, 19, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 749 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035552 none O=C(CN1CCC(=O)NC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 1, 11, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 36, 110, 114, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 35, 110, 110, 114, 114] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31]) total number of confs: 575 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035552 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035552 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035552/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035552 Building REAL250005035553 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035553' /scratch/stefan/7916117/working/building/REAL250005035553 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035553 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035553/0 /scratch/stefan/7916117/working/building/REAL250005035553 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/107 `/scratch/stefan/7916117/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1) `REAL250005035553.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035553 none CC1=CC=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.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, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 11, 11, 11, 45, 48, 116, 116, 116, 116, 116, 1, 1, 6, 6, 6, 6, 2, 6, 6, 11, 45, 45, 48, 48, 1, 1, 1, 1, 6] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 18, 19] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 285 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035553 none CC1=CC=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.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, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 6, 32, 32, 32, 111, 115, 201, 201, 201, 201, 201, 6, 6, 1, 2, 2, 2, 1, 1, 1, 32, 111, 111, 115, 115, 6, 6, 6, 6, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24, 25, 26, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 575 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: REAL250005035553 none CC1=CC=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.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, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 200, 201, 201, 116, 49, 49, 49, 19, 8, 1, 1, 1, 1, 1, 1, 1, 116, 116, 201, 201, 201, 201, 201, 201, 201, 49, 19, 19, 8, 8, 116, 116, 116, 116, 201] 201 rigid atoms, others: [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, 36]) total number of confs: 538 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035553 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035553 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035553/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035553 Building REAL250005035554 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035554' /scratch/stefan/7916117/working/building/REAL250005035554 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035554 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035554/0 /scratch/stefan/7916117/working/building/REAL250005035554 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/108 `/scratch/stefan/7916117/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005035554.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035554 none CC1=CC=CC=C1C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 5, 5, 1, 5, 5, 1, 1, 1, 13, 13, 13, 71, 93, 196, 196, 196, 196, 196, 1, 1, 5, 5, 5, 5, 1, 5, 5, 13, 71, 71, 93, 93, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 36, 6, 7, 8, 19, 20, 35] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 538 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: REAL250005035554 none CC1=CC=CC=C1C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 5, 22, 22, 22, 88, 107, 201, 201, 201, 201, 201, 5, 5, 2, 2, 2, 1, 1, 1, 1, 22, 88, 88, 107, 107, 5, 5, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 567 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035554 none CC1=CC=CC=C1C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 196, 201, 201, 196, 71, 71, 71, 23, 8, 1, 1, 1, 1, 1, 1, 1, 196, 196, 201, 201, 201, 201, 196, 201, 201, 71, 23, 23, 8, 8, 196, 196, 196, 196] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 583 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035554 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035554 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035554/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035554 Building REAL250005035555 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035555' /scratch/stefan/7916117/working/building/REAL250005035555 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035555 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035555/0 /scratch/stefan/7916117/working/building/REAL250005035555 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/109 `/scratch/stefan/7916117/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1) `REAL250005035555.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035555 none C#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 76, 76, 76, 21, 8, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 76, 21, 21, 8, 8, 107] 107 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL250005035555 none C#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 52, 64, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 13, 52, 52, 64, 64, 1] 107 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035555 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035555 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035555/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035555 Building REAL250005035556 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035556' /scratch/stefan/7916117/working/building/REAL250005035556 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035556 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035556/0 /scratch/stefan/7916117/working/building/REAL250005035556 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/110 `/scratch/stefan/7916117/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(F)F)=C1) `REAL250005035556.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035556 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [5, 1, 5, 5, 29, 33, 166, 166, 166, 166, 166, 1, 1, 1, 1, 1, 1, 12, 12, 1, 5, 29, 29, 33, 33, 1, 1, 1, 12, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 19, 25, 26, 27, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 20, 21, 22, 23, 24, 28]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035556 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [56, 56, 17, 8, 1, 1, 1, 1, 1, 1, 1, 56, 166, 166, 70, 166, 166, 201, 201, 166, 56, 17, 17, 8, 8, 166, 166, 98, 201, 166] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 806 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035556 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035556 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035556/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035556 Building REAL250005035557 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035557' /scratch/stefan/7916117/working/building/REAL250005035557 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035557 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035557/0 /scratch/stefan/7916117/working/building/REAL250005035557 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/111 `/scratch/stefan/7916117/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005035557.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035557 none CCC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 12, 39, 39, 39, 104, 104, 196, 196, 196, 196, 196, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 3, 12, 12, 39, 104, 104, 104, 104, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 35, 36, 37, 38, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 570 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: REAL250005035557 none CCC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 187, 147, 46, 46, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 187, 196, 196, 187, 196, 196, 194, 194, 194, 194, 194, 187, 154, 154, 46, 8, 8, 8, 8, 196, 196, 187, 196, 196] 201 rigid atoms, others: [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, 33, 34, 35, 36, 37, 38]) total number of confs: 836 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035557 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035557 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035557/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035557 Building REAL250005035558 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035558' /scratch/stefan/7916117/working/building/REAL250005035558 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035558 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035558/0 /scratch/stefan/7916117/working/building/REAL250005035558 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/112 `/scratch/stefan/7916117/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CC=CC=C21) `REAL250005035558.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035558 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 64, 93, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 64, 64, 93, 93, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 555 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: REAL250005035558 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 201, 201, 83, 25, 25, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 591 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035558 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035558 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035558/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035558 Building REAL250005035559 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035559' /scratch/stefan/7916117/working/building/REAL250005035559 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035559 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035559/0 /scratch/stefan/7916117/working/building/REAL250005035559 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/113 `/scratch/stefan/7916117/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1N=CC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1) `REAL250005035559.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035559 none O=C(CN1N=CC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [49, 49, 49, 143, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 201, 201, 49, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 663 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035559 none O=C(CN1N=CC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 104, 108, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 33, 104, 104, 108, 108] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27] set([0, 1, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 566 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035559 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035559 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035559/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035559 Building REAL250005035560 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035560' /scratch/stefan/7916117/working/building/REAL250005035560 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035560 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035560/0 /scratch/stefan/7916117/working/building/REAL250005035560 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/114 `/scratch/stefan/7916117/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1CCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035560.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035560 none CC1=CC=CC=C1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 152, 143, 51, 51, 51, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 152, 152, 143, 143, 51, 17, 17, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 699 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035560 none CC1=CC=CC=C1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 1, 5, 7, 27, 27, 27, 115, 120, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 5, 5, 7, 7, 27, 117, 117, 120, 120] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 594 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035560 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035560 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035560/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035560 Building REAL250005035561 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035561' /scratch/stefan/7916117/working/building/REAL250005035561 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035561 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035561/0 /scratch/stefan/7916117/working/building/REAL250005035561 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/115 `/scratch/stefan/7916117/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035561.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035561 none COC(=O)NCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 174, 201, 115, 85, 33, 33, 33, 13, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 174, 116, 116, 85, 85, 33, 13, 13, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 789 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035561 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035561 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035561/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035561 Building REAL250005035562 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035562' /scratch/stefan/7916117/working/building/REAL250005035562 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035562 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035562/0 /scratch/stefan/7916117/working/building/REAL250005035562 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/116 `/scratch/stefan/7916117/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CC=CN2N=C1) `REAL250005035562.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035562 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [11, 1, 11, 11, 68, 96, 200, 201, 200, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 67, 67, 96, 96, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) 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: REAL250005035562 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [101, 101, 24, 8, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 201, 201, 200, 200, 100, 25, 25, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035562 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035562 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035562/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035562 Building REAL250005035563 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035563' /scratch/stefan/7916117/working/building/REAL250005035563 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035563 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035563/0 /scratch/stefan/7916117/working/building/REAL250005035563 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/117 `/scratch/stefan/7916117/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(CC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005035563.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035563 none CN1CCN(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 168, 60, 60, 60, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 59, 20, 20, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 700 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035563 none CN1CCN(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 94, 105, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 6, 6, 26, 94, 94, 105, 105, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 17, 18, 35, 22, 23, 24, 25, 36] set([32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 566 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035563 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035563/1 /scratch/stefan/7916117/working/building/REAL250005035563 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/118 `/scratch/stefan/7916117/working/3D/118' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+]1CCN(CC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005035563.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035563 none C[NH+]1CCN(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 23, 23, 23, 11, 7, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 11, 11, 7, 7, 25, 25, 25, 25] 25 rigid atoms, others: [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, 36, 37]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035563 none C[NH+]1CCN(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 9, 9, 9, 15, 15, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 9, 15, 15, 15, 15, 1, 1, 1, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 35] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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/7916117/working/building/REAL250005035563 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035563 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035563/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035563/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035563 Building REAL250005035564 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035564' /scratch/stefan/7916117/working/building/REAL250005035564 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035564 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035564/0 /scratch/stefan/7916117/working/building/REAL250005035564 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/119 `/scratch/stefan/7916117/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)NC2CC2)CCC1) `REAL250005035564.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035564 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)NC2CC2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 26, 33, 111, 111, 111, 111, 111, 1, 1, 4, 4, 4, 15, 15, 1, 1, 1, 6, 26, 26, 33, 33, 4, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 11, 12, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 266 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035564 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)NC2CC2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 17, 8, 1, 1, 1, 1, 1, 1, 1, 62, 111, 159, 159, 159, 201, 201, 111, 111, 111, 62, 17, 17, 8, 8, 159, 201, 201, 201, 201, 201, 111, 111, 111, 111, 111, 111] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 708 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: REAL250005035564 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)NC2CC2)CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 15, 39, 39, 119, 125, 201, 201, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 15, 15, 15, 39, 119, 119, 125, 125, 6, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37]) total number of confs: 611 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035564 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035564 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035564/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035564 Building REAL250005035565 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035565' /scratch/stefan/7916117/working/building/REAL250005035565 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035565 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035565/0 /scratch/stefan/7916117/working/building/REAL250005035565 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/120 `/scratch/stefan/7916117/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+]1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035565.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035565 none CC[N@@H+]1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 78, 78, 78, 78, 78, 78, 78, 62, 62, 62, 17, 8, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 78, 78, 78, 78, 78, 78, 78, 78, 78, 62, 17, 17, 8, 8] 137 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 608 number of broken/clashed sets: 137 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035565 none CC[N@@H+]1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 24, 33, 78, 78, 78, 78, 78, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 24, 24, 33, 33] 137 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 25, 26, 27, 28, 29, 30, 31] set([0, 34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 214 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035565 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035565/1 /scratch/stefan/7916117/working/building/REAL250005035565 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/121 `/scratch/stefan/7916117/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+]1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035565.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035565 none CC[N@H+]1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 63, 63, 63, 63, 63, 63, 63, 54, 54, 54, 17, 9, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 63, 63, 63, 63, 63, 63, 63, 63, 63, 54, 17, 17, 9, 9] 85 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 348 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: REAL250005035565 none CC[N@H+]1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 24, 63, 63, 63, 63, 63, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 24, 24] 85 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 33, 25, 26, 27, 28, 29, 30, 31] set([0, 34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 158 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035565 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035565 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035565/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035565/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035565 Building REAL250005035566 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035566' /scratch/stefan/7916117/working/building/REAL250005035566 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035566 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035566/0 /scratch/stefan/7916117/working/building/REAL250005035566 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/122 `/scratch/stefan/7916117/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1=CC=CC=N1)NCCC1=NC(=O)O[N-]1) `REAL250005035566.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035566 none O=C(CCCC1=CC=CC=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 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: [38, 38, 38, 107, 114, 159, 201, 201, 201, 201, 201, 15, 8, 1, 1, 1, 1, 1, 1, 1, 107, 107, 144, 144, 155, 155, 201, 201, 201, 201, 38, 15, 15, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 927 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035566 none O=C(CCCC1=CC=CC=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 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: [42, 15, 8, 6, 1, 1, 1, 1, 1, 1, 1, 42, 42, 109, 109, 201, 201, 201, 201, 201, 14, 14, 10, 10, 6, 6, 1, 1, 1, 1, 42, 109, 109, 109, 109] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34]) total number of confs: 623 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035566 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035566 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035566/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035566 Building REAL250005035567 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035567' /scratch/stefan/7916117/working/building/REAL250005035567 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035567 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035567/0 /scratch/stefan/7916117/working/building/REAL250005035567 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/123 `/scratch/stefan/7916117/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=CS2)N1) `REAL250005035567.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035567 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=CS2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 14, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [10, 1, 10, 10, 46, 63, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 1, 1, 1, 10, 46, 46, 63, 63, 1, 1, 1, 1] 114 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 348 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035567 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=CS2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 14, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [56, 56, 21, 8, 1, 1, 1, 1, 1, 1, 1, 56, 114, 114, 114, 114, 114, 114, 114, 56, 21, 21, 8, 8, 114, 114, 114, 114] 114 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035567 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035567 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035567/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035567 Building REAL250005035568 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035568' /scratch/stefan/7916117/working/building/REAL250005035568 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035568 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035568/0 /scratch/stefan/7916117/working/building/REAL250005035568 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/124 `/scratch/stefan/7916117/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)N1) `REAL250005035568.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035568 none CC(C)C1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 159, 201, 159, 159, 159, 74, 74, 74, 21, 8, 1, 1, 1, 1, 1, 1, 1, 159, 201, 201, 201, 201, 201, 201, 201, 159, 74, 21, 21, 8, 8, 159] 201 rigid atoms, others: [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]) 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: REAL250005035568 none CC(C)C1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 1, 1, 1, 1, 1, 9, 9, 9, 40, 51, 159, 159, 159, 159, 159, 1, 13, 13, 13, 13, 13, 13, 13, 1, 9, 40, 40, 51, 51, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 18, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035568 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035568 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035568/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035568 Building REAL250005035569 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035569' /scratch/stefan/7916117/working/building/REAL250005035569 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035569 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035569/0 /scratch/stefan/7916117/working/building/REAL250005035569 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/125 `/scratch/stefan/7916117/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=CC=CC2=C1) `REAL250005035569.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035569 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=CC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 5, 5, 37, 65, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 37, 37, 65, 65, 1, 1, 1, 1, 1, 1] 109 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) 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: REAL250005035569 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=CC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [51, 51, 24, 8, 1, 1, 1, 1, 1, 1, 1, 51, 109, 109, 109, 109, 109, 109, 109, 109, 51, 25, 25, 8, 8, 109, 109, 109, 109, 109, 109] 109 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035569 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035569 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035569/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035569 Building REAL250005035570 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035570' /scratch/stefan/7916117/working/building/REAL250005035570 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035570 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035570/0 /scratch/stefan/7916117/working/building/REAL250005035570 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/126 `/scratch/stefan/7916117/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035570.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035570 none COC(=O)NCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 128, 201, 112, 70, 91, 25, 25, 25, 11, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 128, 105, 104, 95, 95, 91, 91, 25, 11, 11, 6, 6] 201 rigid atoms, others: [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]) total number of confs: 938 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035570 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035570 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035570/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035570 Building REAL250005035571 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035571' /scratch/stefan/7916117/working/building/REAL250005035571 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035571 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035571/0 /scratch/stefan/7916117/working/building/REAL250005035571 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/127 `/scratch/stefan/7916117/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N(C)CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035571.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035571 none COC(=O)N(C)CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 142, 201, 114, 142, 90, 98, 33, 33, 33, 13, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 142, 142, 142, 114, 114, 114, 114, 98, 98, 33, 13, 13, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 969 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035571 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035571 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035571/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035571 Building REAL250005035572 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035572' /scratch/stefan/7916117/working/building/REAL250005035572 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035572 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035572/0 /scratch/stefan/7916117/working/building/REAL250005035572 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/128 `/scratch/stefan/7916117/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C1=O) `REAL250005035572.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035572 none CN1C=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 111, 111, 111, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 111, 24, 24, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 462 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035572 none CN1C=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 77, 116, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 13, 77, 77, 116, 116] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 22, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 627 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035572 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035572 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035572/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035572 Building REAL250005035573 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035573' /scratch/stefan/7916117/working/building/REAL250005035573 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035573 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035573/0 /scratch/stefan/7916117/working/building/REAL250005035573 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/129 `/scratch/stefan/7916117/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=C1) `REAL250005035573.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035573 none CSC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 165, 165, 55, 55, 55, 19, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 201, 201, 201, 55, 19, 19, 8, 8, 165, 165] 201 rigid atoms, others: [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]) total number of confs: 408 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: REAL250005035573 none CSC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [7, 1, 1, 1, 1, 12, 12, 12, 65, 71, 165, 165, 165, 165, 165, 1, 1, 1, 7, 7, 7, 12, 65, 65, 71, 71, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 15, 16, 17, 26, 27] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 409 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035573 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035573 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035573/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035573 Building REAL250005035574 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035574' /scratch/stefan/7916117/working/building/REAL250005035574 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035574 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035574/0 /scratch/stefan/7916117/working/building/REAL250005035574 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/130 `/scratch/stefan/7916117/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005035574.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035574 none C#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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, 70, 70, 70, 24, 8, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 70, 24, 24, 8, 8, 95] 95 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035574 none C#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 28, 50, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 5, 28, 28, 50, 50, 1] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035574 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035574 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035574/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035574 Building REAL250005035575 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035575' /scratch/stefan/7916117/working/building/REAL250005035575 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035575 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035575/0 /scratch/stefan/7916117/working/building/REAL250005035575 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/131 `/scratch/stefan/7916117/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CCCCC1)NCCC1=NC(=O)O[N-]1) `REAL250005035575.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035575 none O=C(CC1=CCCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [57, 57, 57, 194, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 194, 194, 201, 201, 201, 201, 201, 201, 201, 201, 201, 57, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 750 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035575 none O=C(CC1=CCCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [33, 7, 1, 1, 1, 1, 1, 1, 1, 33, 33, 105, 107, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 105, 105, 107, 107] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 535 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035575 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035575 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035575/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035575 Building REAL250005035576 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035576' /scratch/stefan/7916117/working/building/REAL250005035576 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035576 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035576/0 /scratch/stefan/7916117/working/building/REAL250005035576 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/132 `/scratch/stefan/7916117/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)NCCC1=NC(=O)O[N-]1)C(C)C) `REAL250005035576.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035576 none CCC(CC(=O)NCCC1=NC(=O)O[N-]1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 67, 67, 67, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 67, 20, 20, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 33, 34, 35, 36, 37]) total number of confs: 801 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035576 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035576 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035576/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035576 Building REAL250005035577 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035577' /scratch/stefan/7916117/working/building/REAL250005035577 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035577 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035577/0 /scratch/stefan/7916117/working/building/REAL250005035577 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/133 `/scratch/stefan/7916117/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2CC2)S1) `REAL250005035577.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035577 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2CC2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 5, 5, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 35, 43, 122, 122, 122, 122, 122, 1, 1, 1, 1, 1, 12, 12, 1, 7, 35, 35, 43, 43, 1, 12, 12, 12, 12, 12] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) 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: REAL250005035577 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2CC2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 5, 5, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [74, 74, 24, 8, 1, 1, 1, 1, 1, 1, 1, 74, 122, 122, 122, 122, 201, 201, 122, 74, 25, 25, 8, 8, 122, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035577 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2CC2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 5, 5, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [54, 12, 54, 54, 130, 140, 201, 201, 201, 201, 201, 12, 12, 12, 1, 1, 1, 1, 12, 54, 130, 130, 140, 140, 12, 1, 1, 1, 1, 1] 201 rigid atoms, others: [14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 620 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035577 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035577 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035577/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035577 Building REAL250005035578 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035578' /scratch/stefan/7916117/working/building/REAL250005035578 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035578 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035578/0 /scratch/stefan/7916117/working/building/REAL250005035578 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/134 `/scratch/stefan/7916117/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21) `REAL250005035578.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035578 none CN1N=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 56, 56, 56, 22, 8, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 107, 107, 55, 22, 22, 8, 8, 107, 107] 107 rigid atoms, others: [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]) total number of confs: 270 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035578 none CN1N=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 35, 58, 107, 107, 107, 107, 107, 1, 1, 1, 2, 2, 2, 1, 7, 35, 35, 58, 58, 1, 1] 107 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 24, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035578 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035578 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035578/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035578 Building REAL250005035579 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035579' /scratch/stefan/7916117/working/building/REAL250005035579 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035579 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035579/0 /scratch/stefan/7916117/working/building/REAL250005035579 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/135 `/scratch/stefan/7916117/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035579.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035579 none CC(C)(C)CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 185, 201, 185, 183, 55, 55, 55, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 183, 183, 55, 17, 17, 8, 8] 201 rigid atoms, others: [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, 36, 37]) total number of confs: 1012 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035579 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035579 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035579/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035579 Building REAL250005035580 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035580' /scratch/stefan/7916117/working/building/REAL250005035580 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035580 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035580/0 /scratch/stefan/7916117/working/building/REAL250005035580 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/136 `/scratch/stefan/7916117/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CSC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035580.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035580 none CC(=O)C1=CSC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 159, 201, 159, 159, 159, 68, 68, 68, 21, 8, 1, 1, 1, 1, 1, 1, 1, 159, 201, 201, 201, 159, 68, 21, 21, 8, 8, 159] 201 rigid atoms, others: [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]) total number of confs: 515 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035580 none CC(=O)C1=CSC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [10, 1, 10, 1, 1, 1, 1, 1, 8, 8, 8, 39, 45, 159, 159, 159, 159, 159, 1, 10, 10, 10, 1, 8, 39, 39, 45, 45, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035580 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035580 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035580/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035580 Building REAL250005035581 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035581' /scratch/stefan/7916117/working/building/REAL250005035581 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035581 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035581/0 /scratch/stefan/7916117/working/building/REAL250005035581 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/137 `/scratch/stefan/7916117/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F) `REAL250005035581.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035581 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 49, 49, 49, 22, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 89, 127, 127, 127, 127, 127, 49, 22, 22, 8, 8, 127, 127] 127 rigid atoms, others: [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]) total number of confs: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035581 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 7, 7, 7, 41, 63, 127, 127, 127, 127, 127, 1, 1, 1, 1, 2, 2, 2, 1, 7, 41, 41, 63, 63, 1, 1] 127 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 22, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035581 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035581 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035581/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035581 Building REAL250005035582 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035582' /scratch/stefan/7916117/working/building/REAL250005035582 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035582 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035582/0 /scratch/stefan/7916117/working/building/REAL250005035582 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/138 `/scratch/stefan/7916117/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=COC2=CC=CC=C12) `REAL250005035582.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035582 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 71, 104, 200, 200, 200, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 71, 71, 104, 104, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 572 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035582 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 24, 8, 1, 1, 1, 1, 1, 1, 1, 95, 200, 201, 201, 201, 201, 201, 201, 201, 94, 24, 24, 8, 8, 200, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035582 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035582 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035582/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035582 Building REAL250005035583 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035583' /scratch/stefan/7916117/working/building/REAL250005035583 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035583 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035583/0 /scratch/stefan/7916117/working/building/REAL250005035583 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/139 `/scratch/stefan/7916117/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1) `REAL250005035583.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035583 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 160, 120, 171, 171, 80, 80, 80, 22, 8, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 201, 201, 201, 171, 171, 80, 23, 23, 8, 8, 171] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 691 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035583 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 42, 64, 171, 171, 171, 171, 171, 1, 1, 1, 2, 2, 2, 1, 1, 7, 42, 42, 64, 64, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 19, 23, 24, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035583 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035583 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035583/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035583 Building REAL250005035584 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035584' /scratch/stefan/7916117/working/building/REAL250005035584 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035584 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035584/0 /scratch/stefan/7916117/working/building/REAL250005035584 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/140 `/scratch/stefan/7916117/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N[C@H](C(=O)NCCC1=NC(=O)O[N-]1)C(C)C) `REAL250005035584.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035584 none COC(=O)N[C@H](C(=O)NCCC1=NC(=O)O[N-]1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 11, 8, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [196, 196, 155, 196, 124, 41, 124, 41, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 118, 148, 151, 196, 196, 196, 155, 40, 8, 8, 8, 8, 153, 153, 153, 153, 153, 153, 153] 201 rigid atoms, others: [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, 36]) total number of confs: 927 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035584 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035584 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035584/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035584 Building REAL250005035585 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035585' /scratch/stefan/7916117/working/building/REAL250005035585 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035585 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035585/0 /scratch/stefan/7916117/working/building/REAL250005035585 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/141 `/scratch/stefan/7916117/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL250005035585.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035585 none CCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 195, 133, 133, 133, 133, 43, 43, 43, 16, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 201, 201, 201, 201, 201, 133, 133, 43, 16, 16, 8, 8, 133, 133, 133, 133] 201 rigid atoms, others: [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, 36]) 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: REAL250005035585 none CCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [19, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 28, 32, 133, 133, 133, 133, 133, 1, 1, 1, 20, 20, 20, 19, 19, 1, 1, 5, 28, 28, 32, 32, 1, 2, 2, 2] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 18, 19, 20, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035585 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035585 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035585/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035585 Building REAL250005035586 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035586' /scratch/stefan/7916117/working/building/REAL250005035586 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035586 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035586/0 /scratch/stefan/7916117/working/building/REAL250005035586 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/142 `/scratch/stefan/7916117/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C2CC2)=N1) `REAL250005035586.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035586 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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: [6, 1, 6, 6, 22, 30, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 1, 13, 13, 1, 6, 22, 22, 30, 30, 1, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035586 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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: [72, 72, 24, 8, 1, 1, 1, 1, 1, 1, 1, 72, 88, 88, 88, 88, 87, 201, 201, 87, 71, 24, 24, 8, 8, 88, 88, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 613 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035586 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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: [40, 13, 40, 40, 94, 111, 201, 201, 201, 201, 201, 13, 13, 13, 13, 1, 1, 1, 1, 13, 40, 94, 94, 111, 111, 13, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 571 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035586 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035586 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035586/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035586 Building REAL250005035587 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035587' /scratch/stefan/7916117/working/building/REAL250005035587 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035587 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035587/0 /scratch/stefan/7916117/working/building/REAL250005035587 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/143 `/scratch/stefan/7916117/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035587.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035587 none CS(=O)(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 23, 30, 30, 19, 23, 17, 17, 17, 10, 7, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 21, 21, 23, 23, 23, 23, 17, 10, 10, 7, 7] 30 rigid atoms, others: [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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035587 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035587 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035587/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035587 Building REAL250005035588 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035588' /scratch/stefan/7916117/working/building/REAL250005035588 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035588 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035588/0 /scratch/stefan/7916117/working/building/REAL250005035588 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/144 `/scratch/stefan/7916117/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035588.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035588 none CC1=NN(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 135, 135, 135, 74, 74, 74, 24, 8, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 135, 74, 24, 24, 8, 8] 135 rigid atoms, others: [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]) total number of confs: 333 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: REAL250005035588 none CC1=NN(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 49, 67, 135, 135, 135, 135, 135, 2, 2, 2, 2, 2, 2, 1, 9, 49, 49, 67, 67] 135 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 392 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035588 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035588 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035588/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035588 Building REAL250005035589 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035589' /scratch/stefan/7916117/working/building/REAL250005035589 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035589 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035589/0 /scratch/stefan/7916117/working/building/REAL250005035589 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/145 `/scratch/stefan/7916117/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005035589.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035589 none CSC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [201, 156, 156, 156, 156, 76, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 156, 201, 201, 201, 156, 156, 76, 24, 24, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL250005035589 none CSC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 41, 53, 156, 156, 156, 156, 156, 1, 12, 12, 12, 1, 1, 8, 41, 41, 53, 53] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 21, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 23, 24, 25, 26, 27]) total number of confs: 353 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035589 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035589 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035589/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035589 Building REAL250005035590 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035590' /scratch/stefan/7916117/working/building/REAL250005035590 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035590 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035590/0 /scratch/stefan/7916117/working/building/REAL250005035590 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/146 `/scratch/stefan/7916117/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035590.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035590 none CC(CC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [170, 68, 170, 201, 201, 201, 201, 201, 201, 68, 68, 21, 8, 1, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 201, 201, 201, 201, 201, 201, 201, 68, 22, 21, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 846 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035590 none CC(CC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 25, 25, 25, 103, 115, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 25, 103, 103, 115, 115] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30] set([0, 32, 34, 35, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 568 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035590 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035590 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035590/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035590 Building REAL250005035591 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035591' /scratch/stefan/7916117/working/building/REAL250005035591 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035591 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035591/0 /scratch/stefan/7916117/working/building/REAL250005035591 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/147 `/scratch/stefan/7916117/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(=O)N(C)C1=O) `REAL250005035591.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035591 none CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(=O)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 115, 115, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 23, 23, 8, 8, 201, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035591 none CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(=O)N(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 76, 115, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 76, 76, 115, 115, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035591 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035591 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035591/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035591 Building REAL250005035592 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035592' /scratch/stefan/7916117/working/building/REAL250005035592 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035592 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035592/0 /scratch/stefan/7916117/working/building/REAL250005035592 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/148 `/scratch/stefan/7916117/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005035592.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035592 none CCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 130, 130, 130, 61, 61, 61, 20, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 201, 201, 201, 201, 201, 130, 60, 20, 20, 8, 8, 130] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 729 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035592 none CCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 5, 5, 5, 29, 42, 130, 130, 130, 130, 130, 1, 1, 9, 9, 9, 9, 9, 1, 5, 29, 29, 42, 42, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 23, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035592 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035592 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035592/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035592 Building REAL250005035593 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035593' /scratch/stefan/7916117/working/building/REAL250005035593 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035593 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035593/0 /scratch/stefan/7916117/working/building/REAL250005035593 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/149 `/scratch/stefan/7916117/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005035593.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035593 none COC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [122, 85, 85, 85, 85, 61, 61, 61, 24, 8, 1, 1, 1, 1, 1, 1, 1, 85, 85, 122, 122, 122, 85, 60, 24, 24, 8, 8, 85] 122 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035593 none COC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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: [2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 37, 85, 85, 85, 85, 85, 1, 1, 3, 3, 3, 1, 4, 21, 21, 37, 37, 1] 122 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 22, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035593 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035593 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035593/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035593 Building REAL250005035594 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035594' /scratch/stefan/7916117/working/building/REAL250005035594 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035594 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035594/0 /scratch/stefan/7916117/working/building/REAL250005035594 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/150 `/scratch/stefan/7916117/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCN1C=CC=CC1=O)NCCC1=NC(=O)O[N-]1) `REAL250005035594.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035594 none O=C(CCCN1C=CC=CC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [38, 38, 38, 130, 136, 178, 201, 201, 201, 201, 201, 201, 16, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 178, 178, 178, 178, 201, 201, 201, 201, 38, 16, 16, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 1066 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035594 none O=C(CCCN1C=CC=CC1=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [27, 7, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 93, 95, 201, 201, 201, 201, 201, 6, 6, 2, 2, 2, 2, 1, 1, 1, 1, 26, 93, 93, 95, 95] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29, 30] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035594 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035594 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035594/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035594 Building REAL250005035595 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035595' /scratch/stefan/7916117/working/building/REAL250005035595 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035595 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035595/0 /scratch/stefan/7916117/working/building/REAL250005035595 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/151 `/scratch/stefan/7916117/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=CC=N2)=C1) `REAL250005035595.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035595 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=CC=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 51, 156, 156, 156, 156, 156, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 5, 29, 29, 51, 51, 1, 1, 1, 7, 7, 7, 1] 201 rigid atoms, others: [1, 33, 11, 12, 13, 14, 15, 16, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32]) total number of confs: 368 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035595 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=CC=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 22, 8, 1, 1, 1, 1, 1, 1, 1, 81, 156, 156, 156, 156, 156, 201, 201, 201, 201, 156, 80, 23, 23, 8, 8, 156, 156, 156, 201, 201, 201, 156] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 461 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035595 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=CC=N2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 19, 19, 72, 94, 201, 201, 201, 201, 201, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 19, 72, 72, 94, 94, 6, 7, 7, 1, 1, 1, 7] 201 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 530 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035595 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035595 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035595/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035595 Building REAL250005035596 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035596' /scratch/stefan/7916117/working/building/REAL250005035596 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035596 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035596/0 /scratch/stefan/7916117/working/building/REAL250005035596 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/152 `/scratch/stefan/7916117/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)[NH+]1CCCCCC1) `REAL250005035596.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035596 none CC(C(=O)NCCC1=NC(=O)O[N-]1)[NH+]1CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.4', 'H', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 17, 17, 17, 58, 64, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 17, 58, 58, 64, 64, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 141 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 40, 41, 39, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 373 number of broken/clashed sets: 88 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035596 none CC(C(=O)NCCC1=NC(=O)O[N-]1)[NH+]1CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.4', 'H', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [129, 69, 69, 69, 17, 8, 1, 1, 1, 1, 1, 1, 1, 129, 141, 141, 141, 141, 141, 141, 141, 129, 129, 129, 129, 69, 17, 17, 8, 8, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141] 141 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 534 number of broken/clashed sets: 88 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035596 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035596 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035596/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035596 Building REAL250005035597 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035597' /scratch/stefan/7916117/working/building/REAL250005035597 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035597 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035597/0 /scratch/stefan/7916117/working/building/REAL250005035597 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/153 `/scratch/stefan/7916117/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(Cl)N=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035597.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035597 none O=C(CC1=CC=C(Cl)N=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 16, 8, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 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: [54, 54, 54, 112, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 112, 112, 201, 201, 201, 54, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035597 none O=C(CC1=CC=C(Cl)N=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 16, 8, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 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: [17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 79, 85, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 17, 79, 79, 85, 85] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 504 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035597 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035597 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035597/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035597 Building REAL250005035598 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035598' /scratch/stefan/7916117/working/building/REAL250005035598 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035598 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035598/0 /scratch/stefan/7916117/working/building/REAL250005035598 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/154 `/scratch/stefan/7916117/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC1=O) `REAL250005035598.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035598 none CCN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 108, 108, 108, 64, 64, 64, 23, 8, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 201, 201, 201, 201, 201, 64, 23, 23, 8, 8, 108, 108] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 841 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035598 none CCN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 12, 12, 12, 53, 57, 108, 108, 108, 108, 108, 1, 1, 1, 1, 6, 6, 6, 5, 5, 12, 53, 53, 57, 57, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 30, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035598 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035598 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035598/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035598 Building REAL250005035599 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035599' /scratch/stefan/7916117/working/building/REAL250005035599 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005035599 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035599/0 /scratch/stefan/7916117/working/building/REAL250005035599 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/155 `/scratch/stefan/7916117/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035599.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035599 none C[N@@H+]1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 53, 53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 53, 17, 17, 8, 8] 58 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL250005035599 none C[N@@H+]1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 26, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 26, 26] 58 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035599 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035599/1 /scratch/stefan/7916117/working/building/REAL250005035599 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/156 `/scratch/stefan/7916117/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035599.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035599 none C[N@H+]1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 53, 53, 53, 17, 9, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 53, 17, 17, 9, 9] 58 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL250005035599 none C[N@H+]1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 26, 58, 58, 58, 58, 58, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 26, 26] 58 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035599 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `2' /scratch/stefan/7916117/working/building/REAL250005035599/2 /scratch/stefan/7916117/working/building/REAL250005035599 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 2 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/157 `/scratch/stefan/7916117/working/3D/157' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035599.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005035599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035599/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035599 none CN1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 125, 125, 87, 87, 87, 24, 8, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 125, 87, 24, 24, 8, 8] 125 rigid atoms, others: [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]) total number of confs: 415 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035599 none CN1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 40, 62, 125, 125, 125, 125, 125, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 40, 40, 62, 62] 125 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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/7916117/working/building/REAL250005035599 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035599 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035599/0.* 2: /scratch/stefan/7916117/working/building/REAL250005035599/2.* 1: /scratch/stefan/7916117/working/building/REAL250005035599/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035599 Building REAL250005035600 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035600' /scratch/stefan/7916117/working/building/REAL250005035600 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035600 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035600/0 /scratch/stefan/7916117/working/building/REAL250005035600 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/158 `/scratch/stefan/7916117/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCCC1OCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035600.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035600 none CC1CCCCC1OCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 161, 50, 51, 51, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 165, 165, 50, 8, 8, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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: REAL250005035600 none CC1CCCCC1OCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 59, 59, 59, 133, 133, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 59, 133, 133, 133, 133] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 629 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035600 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035600 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035600/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035600 Building REAL250005035601 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035601' /scratch/stefan/7916117/working/building/REAL250005035601 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035601 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035601/0 /scratch/stefan/7916117/working/building/REAL250005035601 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/159 `/scratch/stefan/7916117/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCOCC1)NCCC1=NC(=O)O[N-]1) `REAL250005035601.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035601 none O=C(CC1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [60, 60, 60, 178, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 178, 178, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 766 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035601 none O=C(CC1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 7, 1, 1, 1, 1, 1, 1, 1, 28, 28, 101, 107, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 101, 101, 107, 107] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035601 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035601 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035601/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035601 Building REAL250005035602 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035602' /scratch/stefan/7916117/working/building/REAL250005035602 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035602 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035602/0 /scratch/stefan/7916117/working/building/REAL250005035602 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/160 `/scratch/stefan/7916117/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035602.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035602 none CCC(CC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 149, 70, 149, 198, 198, 198, 198, 198, 198, 70, 70, 21, 8, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 173, 149, 198, 198, 198, 198, 198, 198, 198, 70, 21, 22, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1063 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035602 none CCC(CC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [7, 5, 2, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 71, 88, 198, 198, 198, 198, 198, 7, 7, 7, 7, 7, 5, 2, 2, 1, 1, 1, 1, 1, 17, 71, 71, 88, 88] 201 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: 535 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035602 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035602 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035602/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035602 Building REAL250005035603 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035603' /scratch/stefan/7916117/working/building/REAL250005035603 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035603 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035603/0 /scratch/stefan/7916117/working/building/REAL250005035603 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/161 `/scratch/stefan/7916117/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C(C)C) `REAL250005035603.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035603 none COC(=O)NC(C(=O)NCCC1=NC(=O)O[N-]1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 155, 196, 124, 39, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 117, 151, 148, 196, 196, 196, 155, 124, 38, 8, 8, 8, 8, 153, 153, 153, 153, 153, 153, 153] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 938 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035603 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035603 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035603/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035603 Building REAL250005035604 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035604' /scratch/stefan/7916117/working/building/REAL250005035604 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035604 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035604/0 /scratch/stefan/7916117/working/building/REAL250005035604 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/162 `/scratch/stefan/7916117/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1COC2=CC=CC=C21) `REAL250005035604.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035604 none O=C(NCCC1=NC(=O)O[N-]1)C1COC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 60, 92, 196, 196, 196, 196, 196, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 60, 60, 92, 92, 1, 1, 1, 1, 1, 1, 1] 196 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 543 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: REAL250005035604 none O=C(NCCC1=NC(=O)O[N-]1)C1COC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 91, 196, 196, 196, 196, 196, 196, 196, 196, 91, 24, 24, 8, 8, 196, 196, 196, 196, 196, 196, 196] 196 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 581 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035604 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035604 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035604/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035604 Building REAL250005035605 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035605' /scratch/stefan/7916117/working/building/REAL250005035605 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035605 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035605/0 /scratch/stefan/7916117/working/building/REAL250005035605 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/163 `/scratch/stefan/7916117/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1F) `REAL250005035605.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035605 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 28, 28, 28, 95, 107, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 28, 95, 95, 107, 107, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 575 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035605 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 68, 68, 68, 21, 8, 1, 1, 1, 1, 1, 1, 1, 165, 201, 201, 201, 201, 201, 201, 165, 165, 165, 165, 68, 22, 22, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035605 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035605 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035605/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035605 Building REAL250005035606 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035606' /scratch/stefan/7916117/working/building/REAL250005035606 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035606 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035606/0 /scratch/stefan/7916117/working/building/REAL250005035606 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/164 `/scratch/stefan/7916117/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOCC1) `REAL250005035606.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035606 none N#CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOCC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 93, 93, 93, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 93, 19, 19, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 600 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035606 none N#CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOCC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 7, 7, 7, 46, 84, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 7, 46, 46, 84, 84, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035606 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035606 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035606/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035606 Building REAL250005035607 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035607' /scratch/stefan/7916117/working/building/REAL250005035607 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035607 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035607/0 /scratch/stefan/7916117/working/building/REAL250005035607 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/165 `/scratch/stefan/7916117/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(NS(C)(=O)=O)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035607.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035607 none CC(C)(NS(C)(=O)=O)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 5, 11, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 6, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [141, 76, 141, 143, 169, 169, 169, 169, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 141, 143, 141, 143, 169, 169, 169, 169, 75, 25, 24, 8, 8] 169 rigid atoms, others: [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]) total number of confs: 691 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035607 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035607 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035607/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035607 Building REAL250005035608 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035608' /scratch/stefan/7916117/working/building/REAL250005035608 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035608 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035608/0 /scratch/stefan/7916117/working/building/REAL250005035608 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/166 `/scratch/stefan/7916117/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=CN1) `REAL250005035608.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035608 none CC1=CC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 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, 99, 99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 170, 170, 99, 24, 24, 8, 8, 170, 170] 170 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035608 none CC1=CC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 73, 98, 170, 170, 170, 170, 170, 1, 1, 2, 2, 2, 1, 13, 73, 73, 98, 98, 1, 1] 170 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 22, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 531 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035608 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035608 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035608/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035608 Building REAL250005035609 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035609' /scratch/stefan/7916117/working/building/REAL250005035609 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005035609 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035609/0 /scratch/stefan/7916117/working/building/REAL250005035609 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/167 `/scratch/stefan/7916117/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035609.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035609 none CCN1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 141, 141, 141, 141, 141, 70, 70, 70, 21, 8, 1, 1, 1, 1, 1, 1, 1, 141, 201, 201, 201, 201, 201, 141, 141, 141, 141, 141, 69, 21, 21, 8, 8, 141, 141] 201 rigid atoms, others: [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]) total number of confs: 782 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: REAL250005035609 none CCN1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 49, 55, 141, 141, 141, 141, 141, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 13, 49, 49, 55, 55, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 18, 35, 24, 25, 26, 27, 28] set([0, 32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 29, 30, 31]) total number of confs: 335 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035609 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035609/1 /scratch/stefan/7916117/working/building/REAL250005035609 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/168 `/scratch/stefan/7916117/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+]1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035609.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035609 none CC[N@@H+]1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 19, 19, 19, 19, 19, 19, 15, 15, 15, 13, 9, 1, 1, 1, 1, 1, 1, 1, 19, 29, 29, 29, 29, 29, 19, 19, 19, 19, 19, 15, 13, 13, 9, 9, 19, 19] 29 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 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: REAL250005035609 none CC[N@@H+]1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 19, 19, 19, 19, 19, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 1, 1] 29 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 36, 19, 25, 26, 27, 28, 29, 35] set([0, 32, 34, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 67 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035609 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `2' /scratch/stefan/7916117/working/building/REAL250005035609/2 /scratch/stefan/7916117/working/building/REAL250005035609 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 2 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/169 `/scratch/stefan/7916117/working/3D/169' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+]1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035609.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005035609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035609/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035609 none CC[N@H+]1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 18, 18, 18, 18, 18, 18, 14, 14, 14, 12, 9, 1, 1, 1, 1, 1, 1, 1, 18, 28, 28, 28, 28, 28, 18, 18, 18, 18, 18, 14, 12, 12, 9, 9, 18, 18] 28 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 121 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: REAL250005035609 none CC[N@H+]1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 18, 18, 18, 18, 18, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 1, 1] 28 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 36, 19, 25, 26, 27, 28, 29, 35] set([0, 32, 34, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 30, 31]) total number of confs: 64 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035609 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035609 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035609/0.* 2: /scratch/stefan/7916117/working/building/REAL250005035609/2.* 1: /scratch/stefan/7916117/working/building/REAL250005035609/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035609 Building REAL250005035610 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035610' /scratch/stefan/7916117/working/building/REAL250005035610 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035610 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035610/0 /scratch/stefan/7916117/working/building/REAL250005035610 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/170 `/scratch/stefan/7916117/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CC([N+](=O)[O-])=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035610.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035610 none O=C(CC1=CC=CC([N+](=O)[O-])=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 5, 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: [51, 51, 51, 126, 201, 201, 168, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 168, 201, 51, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035610 none O=C(CC1=CC=CC([N+](=O)[O-])=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 5, 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: [17, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 17, 17, 79, 87, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 17, 79, 79, 87, 87] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 11, 23, 24, 25, 26] set([0, 1, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 528 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035610 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035610 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035610/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035610 Building REAL250005035611 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035611' /scratch/stefan/7916117/working/building/REAL250005035611 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035611 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035611/0 /scratch/stefan/7916117/working/building/REAL250005035611 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/171 `/scratch/stefan/7916117/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NO1) `REAL250005035611.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035611 none CC(C)(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 128, 201, 201, 128, 128, 80, 80, 80, 24, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 79, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 780 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035611 none CC(C)(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [4, 1, 4, 4, 1, 1, 1, 1, 13, 13, 13, 46, 68, 128, 128, 128, 128, 128, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 13, 46, 46, 68, 68] 201 rigid atoms, others: [1, 4, 5, 6, 7, 18, 19, 29] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035611 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035611 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035611/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035611 Building REAL250005035612 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035612' /scratch/stefan/7916117/working/building/REAL250005035612 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035612 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035612/0 /scratch/stefan/7916117/working/building/REAL250005035612 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/172 `/scratch/stefan/7916117/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1) `REAL250005035612.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035612 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 163, 143, 163, 163, 67, 67, 67, 19, 8, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 201, 201, 201, 163, 163, 67, 20, 20, 8, 8, 163, 163, 163, 163] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 528 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035612 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 48, 62, 163, 163, 163, 163, 163, 1, 1, 1, 3, 3, 3, 1, 1, 9, 48, 48, 62, 62, 2, 2, 2, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 17, 18, 19, 23, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035612 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035612 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035612/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035612 Building REAL250005035613 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035613' /scratch/stefan/7916117/working/building/REAL250005035613 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035613 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035613/0 /scratch/stefan/7916117/working/building/REAL250005035613 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/173 `/scratch/stefan/7916117/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C)=C1NCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035613.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035613 none CC1=CC=CC(C)=C1NCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 175, 55, 55, 55, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 55, 19, 19, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 751 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: REAL250005035613 none CC1=CC=CC(C)=C1NCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 42, 42, 42, 109, 109, 200, 200, 200, 200, 200, 2, 2, 2, 1, 1, 1, 2, 2, 2, 3, 9, 9, 42, 109, 109, 109, 109] 200 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 581 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035613 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035613 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035613/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035613 Building REAL250005035614 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035614' /scratch/stefan/7916117/working/building/REAL250005035614 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035614 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035614/0 /scratch/stefan/7916117/working/building/REAL250005035614 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/174 `/scratch/stefan/7916117/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035614.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035614 none CC1CCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 89, 89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 201, 88, 24, 24, 8, 8, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 613 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035614 none CC1CCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 12, 12, 12, 61, 95, 200, 200, 200, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 61, 61, 95, 95, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 17, 35, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 29, 30, 31]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035614 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035614 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035614/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035614 Building REAL250005035615 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035615' /scratch/stefan/7916117/working/building/REAL250005035615 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035615 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035615/0 /scratch/stefan/7916117/working/building/REAL250005035615 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/175 `/scratch/stefan/7916117/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C([N+](=O)[O-])C(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035615.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035615 none CC1=CC=C([N+](=O)[O-])C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 97, 85, 97, 97, 97, 97, 97, 85, 85, 85, 23, 8, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 85, 97, 85, 23, 23, 8, 8, 97] 97 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035615 none CC1=CC=C([N+](=O)[O-])C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 7, 7, 23, 37, 97, 97, 97, 97, 97, 1, 2, 2, 2, 1, 1, 7, 23, 23, 37, 37, 1] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 20, 24, 25, 31] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035615 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035615 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035615/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035615 Building REAL250005035616 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035616' /scratch/stefan/7916117/working/building/REAL250005035616 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035616 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035616/0 /scratch/stefan/7916117/working/building/REAL250005035616 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/176 `/scratch/stefan/7916117/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=CO1) `REAL250005035616.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035616 none CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 107, 108, 108, 24, 8, 1, 1, 1, 1, 1, 1, 1, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 107, 24, 24, 8, 8, 200] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 459 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: REAL250005035616 none CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 11, 11, 11, 55, 83, 201, 201, 201, 200, 200, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 55, 55, 83, 83, 1] 201 rigid atoms, others: [1, 3, 4, 5, 16, 17, 18, 31] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 529 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035616 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035616 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035616/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035616 Building REAL250005035617 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035617' /scratch/stefan/7916117/working/building/REAL250005035617 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035617 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035617/0 /scratch/stefan/7916117/working/building/REAL250005035617 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/177 `/scratch/stefan/7916117/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=C2)N1) `REAL250005035617.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035617 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 35, 49, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 9, 35, 35, 49, 49, 1, 1, 7, 7, 1, 7, 7, 1] 201 rigid atoms, others: [1, 34, 11, 12, 13, 14, 15, 21, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035617 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 83, 126, 126, 126, 126, 201, 201, 126, 201, 201, 126, 83, 24, 24, 8, 8, 126, 126, 201, 201, 126, 201, 201, 126] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 664 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035617 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2=CC=CC=C2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 6, 38, 38, 103, 117, 201, 201, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 38, 103, 103, 117, 117, 6, 7, 1, 1, 1, 1, 1, 7] 201 rigid atoms, others: [32, 33, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 578 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035617 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035617 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035617/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035617 Building REAL250005035618 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035618' /scratch/stefan/7916117/working/building/REAL250005035618 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035618 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035618/0 /scratch/stefan/7916117/working/building/REAL250005035618 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/178 `/scratch/stefan/7916117/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C=C1CCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035618.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035618 none CC1=NN(C)C=C1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 123, 112, 41, 41, 41, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 123, 123, 112, 112, 41, 17, 17, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 663 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035618 none CC1=NN(C)C=C1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 1, 6, 10, 34, 34, 34, 108, 110, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 1, 6, 6, 10, 10, 34, 110, 110, 110, 110] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035618 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035618 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035618/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035618 Building REAL250005035619 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035619' /scratch/stefan/7916117/working/building/REAL250005035619 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035619 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035619/0 /scratch/stefan/7916117/working/building/REAL250005035619 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/179 `/scratch/stefan/7916117/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CCCO2)OC=N1) `REAL250005035619.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035619 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CCCO2)OC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 5, 12, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [7, 1, 7, 7, 35, 55, 156, 156, 156, 156, 156, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 7, 35, 35, 55, 55, 6, 6, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [1, 33, 11, 12, 13, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035619 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CCCO2)OC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 5, 12, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [110, 110, 24, 8, 1, 1, 1, 1, 1, 1, 1, 110, 156, 156, 201, 201, 201, 201, 156, 155, 156, 109, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201, 156] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 582 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035619 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(C2CCCO2)OC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 5, 12, 12, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [21, 6, 21, 21, 73, 93, 201, 201, 201, 201, 201, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 21, 73, 73, 93, 93, 1, 1, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 533 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035619 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035619 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035619/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035619 Building REAL250005035620 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035620' /scratch/stefan/7916117/working/building/REAL250005035620 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035620 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035620/0 /scratch/stefan/7916117/working/building/REAL250005035620 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/180 `/scratch/stefan/7916117/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1) `REAL250005035620.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035620 none CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 12, 55, 55, 55, 120, 120, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 12, 12, 55, 120, 120, 120, 120, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 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: REAL250005035620 none CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 120, 44, 44, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 152, 201, 201, 201, 201, 201, 201, 152, 152, 152, 151, 126, 126, 43, 8, 8, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035620 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035620 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035620/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035620 Building REAL250005035621 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035621' /scratch/stefan/7916117/working/building/REAL250005035621 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035621 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035621/0 /scratch/stefan/7916117/working/building/REAL250005035621 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/181 `/scratch/stefan/7916117/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CCC(=O)NCCC2=NC(=O)O[N-]2)=CS1) `REAL250005035621.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035621 none CC1=NC(CCC(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 111, 38, 38, 38, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 135, 135, 111, 111, 38, 15, 15, 7, 7, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL250005035621 none CC1=NC(CCC(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 6, 12, 47, 47, 47, 121, 121, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 6, 6, 12, 12, 47, 121, 121, 121, 121, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035621 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035621 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035621/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035621 Building REAL250005035622 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035622' /scratch/stefan/7916117/working/building/REAL250005035622 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035622 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035622/0 /scratch/stefan/7916117/working/building/REAL250005035622 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/182 `/scratch/stefan/7916117/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1C) `REAL250005035622.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035622 none CC(=CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 101, 115, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 26, 101, 101, 115, 115, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 1, 33, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) 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: REAL250005035622 none CC(=CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 126, 59, 59, 59, 19, 8, 1, 1, 1, 1, 1, 1, 1, 132, 201, 201, 175, 201, 201, 201, 132, 132, 132, 132, 59, 19, 19, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 710 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035622 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035622 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035622/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035622 Building REAL250005035623 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035623' /scratch/stefan/7916117/working/building/REAL250005035623 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035623 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035623/0 /scratch/stefan/7916117/working/building/REAL250005035623 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/183 `/scratch/stefan/7916117/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1CCOCC1)NCCC1=NC(=O)O[N-]1) `REAL250005035623.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035623 none O=C(COC1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 162, 190, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 164, 164, 201, 201, 201, 201, 201, 201, 201, 201, 201, 61, 19, 19, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 728 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035623 none O=C(COC1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [47, 15, 5, 1, 1, 1, 1, 1, 1, 1, 47, 47, 103, 107, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 103, 103, 107, 107] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 34, 33, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035623 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035623 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035623/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035623 Building REAL250005035624 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035624' /scratch/stefan/7916117/working/building/REAL250005035624 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035624 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035624/0 /scratch/stefan/7916117/working/building/REAL250005035624 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/184 `/scratch/stefan/7916117/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(CC)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035624.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035624 none CCCCC(CC)CC(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 193, 152, 108, 150, 179, 35, 35, 35, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 193, 193, 156, 179, 173, 179, 179, 179, 108, 108, 35, 17, 17, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1096 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035624 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035624 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035624/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035624 Building REAL250005035625 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035625' /scratch/stefan/7916117/working/building/REAL250005035625 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035625 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035625/0 /scratch/stefan/7916117/working/building/REAL250005035625 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/185 `/scratch/stefan/7916117/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1) `REAL250005035625.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035625 none O=C(CC1CCC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [55, 55, 55, 186, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 186, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 55, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 774 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035625 none O=C(CC1CCC2=CC=CC=C21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 107, 117, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 107, 107, 117, 117] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 35, 36, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 581 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035625 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035625 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035625/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035625 Building REAL250005035626 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035626' /scratch/stefan/7916117/working/building/REAL250005035626 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035626 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035626/0 /scratch/stefan/7916117/working/building/REAL250005035626 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/186 `/scratch/stefan/7916117/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC(OCC(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035626.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035626 none CC1CCCC(OCC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 186, 132, 47, 47, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 138, 46, 9, 8, 8, 8, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 644 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035626 none CC1CCCC(OCC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 17, 72, 72, 72, 129, 129, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 72, 129, 129, 129, 129, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035626 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035626 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035626/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035626 Building REAL250005035627 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035627' /scratch/stefan/7916117/working/building/REAL250005035627 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035627 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035627/0 /scratch/stefan/7916117/working/building/REAL250005035627 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/187 `/scratch/stefan/7916117/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035627.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035627 none CC1=CC=CC=C1C(C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 200, 201, 201, 200, 156, 200, 55, 55, 55, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 200, 201, 201, 200, 200, 200, 200, 163, 163, 54, 9, 9, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 793 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035627 none CC1=CC=CC=C1C(C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 4, 4, 15, 55, 55, 55, 124, 124, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 15, 15, 55, 124, 124, 124, 124] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 612 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035627 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035627 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035627/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035627 Building REAL250005035628 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035628' /scratch/stefan/7916117/working/building/REAL250005035628 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035628 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035628/0 /scratch/stefan/7916117/working/building/REAL250005035628 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/188 `/scratch/stefan/7916117/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CSC2=CC=CC=C21) `REAL250005035628.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035628 none O=C(NCCC1=NC(=O)O[N-]1)C1CSC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 61, 90, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 61, 61, 90, 90, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 546 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035628 none O=C(NCCC1=NC(=O)O[N-]1)C1CSC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 201, 201, 83, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 577 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035628 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035628 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035628/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035628 Building REAL250005035629 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035629' /scratch/stefan/7916117/working/building/REAL250005035629 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035629 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035629/0 /scratch/stefan/7916117/working/building/REAL250005035629 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/189 `/scratch/stefan/7916117/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCS(=O)(=O)CC1) `REAL250005035629.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035629 none O=C(NCCC1=NC(=O)O[N-]1)C1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 14, 11, 11, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 65, 101, 195, 195, 195, 195, 195, 1, 1, 1, 1, 1, 1, 1, 1, 12, 65, 65, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1, 1] 195 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 574 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: REAL250005035629 none O=C(NCCC1=NC(=O)O[N-]1)C1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 14, 11, 11, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 24, 8, 1, 1, 1, 1, 1, 1, 1, 106, 195, 195, 195, 195, 195, 195, 195, 105, 24, 24, 8, 8, 195, 195, 195, 195, 195, 195, 195, 195, 195] 195 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 604 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035629 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035629 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035629/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035629 Building REAL250005035630 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035630' /scratch/stefan/7916117/working/building/REAL250005035630 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035630 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035630/0 /scratch/stefan/7916117/working/building/REAL250005035630 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/190 `/scratch/stefan/7916117/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCSCC1) `REAL250005035630.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035630 none O=C(NCCC1=NC(=O)O[N-]1)C1CCSCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 74, 118, 197, 197, 197, 197, 197, 1, 1, 1, 1, 1, 1, 13, 74, 74, 118, 118, 1, 1, 1, 1, 1, 1, 1, 1, 1] 197 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 624 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: REAL250005035630 none O=C(NCCC1=NC(=O)O[N-]1)C1CCSCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 24, 8, 1, 1, 1, 1, 1, 1, 1, 108, 197, 197, 197, 197, 197, 108, 25, 24, 8, 8, 197, 197, 197, 197, 197, 197, 197, 197, 197] 197 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 590 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035630 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035630 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035630/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035630 Building REAL250005035631 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035631' /scratch/stefan/7916117/working/building/REAL250005035631 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035631 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035631/0 /scratch/stefan/7916117/working/building/REAL250005035631 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/191 `/scratch/stefan/7916117/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005035631.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035631 none CC(C)N1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 167, 201, 167, 167, 167, 92, 92, 92, 24, 8, 1, 1, 1, 1, 1, 1, 1, 167, 201, 201, 201, 201, 201, 201, 201, 167, 167, 92, 25, 25, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035631 none CC(C)N1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [13, 1, 13, 1, 1, 1, 1, 1, 6, 6, 6, 35, 51, 167, 167, 167, 167, 167, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1, 6, 35, 35, 52, 52] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035631 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035631 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035631/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035631 Building REAL250005035632 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035632' /scratch/stefan/7916117/working/building/REAL250005035632 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035632 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035632/0 /scratch/stefan/7916117/working/building/REAL250005035632 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/192 `/scratch/stefan/7916117/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035632.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035632 none CC(CC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 57, 161, 197, 201, 201, 201, 201, 201, 57, 57, 8, 8, 1, 1, 1, 1, 1, 1, 1, 164, 159, 164, 164, 196, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 56, 8, 8, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 799 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: REAL250005035632 none CC(CC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 7, 1, 1, 1, 1, 1, 1, 1, 14, 55, 55, 55, 122, 122, 201, 201, 201, 201, 201, 14, 14, 14, 14, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 122, 122, 122, 122] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 37, 38, 39, 40, 41]) total number of confs: 586 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035632 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035632 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035632/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035632 Building REAL250005035633 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035633' /scratch/stefan/7916117/working/building/REAL250005035633 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035633 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035633/0 /scratch/stefan/7916117/working/building/REAL250005035633 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/193 `/scratch/stefan/7916117/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005035633.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035633 none CC1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 177, 55, 55, 55, 17, 8, 1, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 177, 177, 55, 17, 17, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL250005035633 none CC1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 97, 101, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 29, 97, 97, 101, 101, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 17, 18, 35, 22, 23, 24, 25, 26, 27, 37, 36] set([32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035633 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035633 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035633/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035633 Building REAL250005035634 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035634' /scratch/stefan/7916117/working/building/REAL250005035634 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035634 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035634/0 /scratch/stefan/7916117/working/building/REAL250005035634 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/194 `/scratch/stefan/7916117/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(COCC(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005035634.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035634 none CC1=NOC(COCC(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 123, 78, 65, 27, 27, 27, 7, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 123, 123, 74, 74, 27, 7, 7, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 634 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035634 none CC1=NOC(COCC(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 31, 60, 73, 73, 73, 124, 124, 201, 201, 201, 201, 201, 1, 2, 2, 2, 8, 8, 59, 59, 73, 124, 124, 124, 124] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035634 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035634 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035634/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035634 Building REAL250005035635 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035635' /scratch/stefan/7916117/working/building/REAL250005035635 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035635 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035635/0 /scratch/stefan/7916117/working/building/REAL250005035635 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/195 `/scratch/stefan/7916117/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1CCCC1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035635.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035635 none CC(CC1CCCC1)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 56, 153, 201, 201, 201, 201, 201, 56, 56, 19, 8, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 56, 19, 19, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL250005035635 none CC(CC1CCCC1)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 1, 8, 28, 28, 28, 103, 109, 201, 201, 201, 201, 201, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 103, 103, 109, 109] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38]) total number of confs: 566 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035635 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035635 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035635/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035635 Building REAL250005035636 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035636' /scratch/stefan/7916117/working/building/REAL250005035636 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035636 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035636/0 /scratch/stefan/7916117/working/building/REAL250005035636 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/196 `/scratch/stefan/7916117/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1CCCCO1)NCCC1=NC(=O)O[N-]1) `REAL250005035636.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035636 none O=C(CCC1CCCCO1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 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: [59, 58, 58, 150, 160, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 150, 150, 182, 182, 195, 201, 201, 201, 201, 201, 201, 201, 201, 58, 19, 19, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 910 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035636 none O=C(CCC1CCCCO1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 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: [42, 12, 7, 1, 1, 1, 1, 1, 1, 1, 42, 42, 102, 105, 201, 201, 201, 201, 201, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 102, 102, 105, 105] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 36, 33, 35, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 571 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035636 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035636 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035636/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035636 Building REAL250005035637 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035637' /scratch/stefan/7916117/working/building/REAL250005035637 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035637 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035637/0 /scratch/stefan/7916117/working/building/REAL250005035637 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/197 `/scratch/stefan/7916117/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC1CCCC1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035637.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035637 none CCC(OC1CCCC1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 120, 45, 120, 140, 172, 172, 172, 172, 45, 45, 15, 7, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 120, 172, 172, 172, 172, 172, 172, 172, 172, 172, 45, 15, 15, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 898 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035637 none CCC(OC1CCCC1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 10, 6, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 80, 86, 172, 172, 172, 172, 172, 19, 19, 19, 19, 19, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 80, 80, 86, 86] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39]) total number of confs: 535 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035637 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035637 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035637/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035637 Building REAL250005035638 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035638' /scratch/stefan/7916117/working/building/REAL250005035638 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035638 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035638/0 /scratch/stefan/7916117/working/building/REAL250005035638 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/198 `/scratch/stefan/7916117/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035638.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035638 none CC(OC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 54, 142, 184, 201, 201, 201, 201, 201, 54, 54, 17, 7, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 54, 17, 17, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 684 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035638 none CC(OC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 10, 39, 39, 39, 117, 118, 201, 201, 201, 201, 201, 11, 11, 11, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 117, 117, 118, 118] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 35, 36, 37, 38, 39]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035638 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035638 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035638/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035638 Building REAL250005035639 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035639' /scratch/stefan/7916117/working/building/REAL250005035639 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035639 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035639/0 /scratch/stefan/7916117/working/building/REAL250005035639 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/199 `/scratch/stefan/7916117/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1) `REAL250005035639.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035639 none N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 70, 70, 70, 21, 8, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 70, 21, 21, 8, 8, 107] 107 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035639 none N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 52, 63, 107, 107, 107, 107, 107, 1, 1, 1, 1, 13, 52, 52, 63, 63, 1] 107 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035639 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035639 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035639/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035639 Building REAL250005035640 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035640' /scratch/stefan/7916117/working/building/REAL250005035640 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035640 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035640/0 /scratch/stefan/7916117/working/building/REAL250005035640 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/200 `/scratch/stefan/7916117/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NOC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035640.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035640 none CC(C)C1=NOC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 151, 201, 151, 151, 151, 76, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 151, 201, 201, 201, 201, 201, 201, 201, 76, 24, 24, 8, 8, 151] 201 rigid atoms, others: [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]) 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: REAL250005035640 none CC(C)C1=NOC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 1, 5, 1, 1, 1, 1, 1, 8, 8, 8, 40, 57, 151, 151, 151, 151, 151, 1, 5, 5, 5, 5, 5, 5, 5, 8, 40, 40, 57, 57, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035640 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035640 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035640/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035640 Building REAL250005035641 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035641' /scratch/stefan/7916117/working/building/REAL250005035641 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035641 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035641/0 /scratch/stefan/7916117/working/building/REAL250005035641 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/201 `/scratch/stefan/7916117/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035641.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035641 none COC1=CC=C(C(C)C(=O)NCCC2=NC(=O)O[N-]2)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 191, 201, 201, 162, 65, 162, 65, 65, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 162, 162, 162, 162, 64, 19, 19, 8, 8, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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: REAL250005035641 none COC1=CC=C(C(C)C(=O)NCCC2=NC(=O)O[N-]2)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 8, 8, 30, 30, 30, 105, 114, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 30, 105, 105, 114, 114, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 36, 35] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31]) total number of confs: 598 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035641 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035641 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035641/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035641 Building REAL250005035642 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035642' /scratch/stefan/7916117/working/building/REAL250005035642 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035642 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035642/0 /scratch/stefan/7916117/working/building/REAL250005035642 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/202 `/scratch/stefan/7916117/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1) `REAL250005035642.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035642 none CN(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 188, 201, 188, 188, 67, 67, 67, 19, 8, 1, 1, 1, 1, 1, 1, 1, 188, 188, 188, 201, 201, 201, 201, 201, 201, 188, 67, 19, 19, 8, 8, 188, 188] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 439 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035642 none CN(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [6, 1, 6, 1, 1, 1, 1, 5, 5, 5, 29, 39, 188, 188, 188, 188, 188, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 5, 29, 29, 39, 39, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 33, 17, 18, 19, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 339 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035642 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035642 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035642/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035642 Building REAL250005035643 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035643' /scratch/stefan/7916117/working/building/REAL250005035643 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035643 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035643/0 /scratch/stefan/7916117/working/building/REAL250005035643 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/203 `/scratch/stefan/7916117/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1CCCC1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035643.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035643 none CC(OC1CCCC1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [148, 52, 148, 181, 201, 201, 201, 201, 52, 52, 17, 7, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 52, 17, 17, 7, 7] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 698 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035643 none CC(OC1CCCC1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [14, 6, 1, 1, 1, 1, 1, 1, 14, 42, 42, 42, 118, 119, 201, 201, 201, 201, 201, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 118, 118, 119, 119] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035643 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035643 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035643/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035643 Building REAL250005035644 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035644' /scratch/stefan/7916117/working/building/REAL250005035644 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035644 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035644/0 /scratch/stefan/7916117/working/building/REAL250005035644 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/204 `/scratch/stefan/7916117/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC2CCC1O2) `REAL250005035644.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035644 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2CCC1O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 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, 24, 39, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 93 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 248 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: REAL250005035644 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2CCC1O2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 22, 8, 1, 1, 1, 1, 1, 1, 1, 64, 93, 93, 93, 93, 93, 93, 64, 22, 22, 8, 8, 93, 93, 93, 93, 93, 93, 93, 93, 93] 93 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 331 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035644 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035644 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035644/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035644 Building REAL250005035645 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035645' /scratch/stefan/7916117/working/building/REAL250005035645 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035645 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035645/0 /scratch/stefan/7916117/working/building/REAL250005035645 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/205 `/scratch/stefan/7916117/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C)=C1) `REAL250005035645.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035645 none COC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 173, 173, 75, 75, 75, 22, 8, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 201, 201, 201, 74, 23, 23, 8, 8, 173, 173, 173, 173] 201 rigid atoms, others: [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]) total number of confs: 438 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035645 none COC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [4, 1, 1, 1, 1, 12, 12, 12, 54, 72, 173, 173, 173, 173, 173, 1, 1, 1, 1, 4, 4, 4, 12, 54, 54, 72, 72, 2, 2, 2, 1] 201 rigid atoms, others: [1, 2, 3, 4, 15, 16, 17, 18, 30] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035645 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035645 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035645/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035645 Building REAL250005035646 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035646' /scratch/stefan/7916117/working/building/REAL250005035646 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035646 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035646/0 /scratch/stefan/7916117/working/building/REAL250005035646 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/206 `/scratch/stefan/7916117/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035646.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035646 none CNC(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 171, 201, 171, 171, 171, 171, 73, 73, 73, 19, 8, 1, 1, 1, 1, 1, 1, 1, 171, 201, 201, 201, 201, 171, 171, 171, 73, 19, 19, 8, 8, 171] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035646 none CNC(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 41, 171, 171, 171, 171, 171, 1, 5, 5, 5, 5, 1, 1, 1, 5, 29, 29, 41, 41, 1] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 9, 20, 25, 26, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035646 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035646 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035646/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035646 Building REAL250005035647 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035647' /scratch/stefan/7916117/working/building/REAL250005035647 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035647 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035647/0 /scratch/stefan/7916117/working/building/REAL250005035647 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/207 `/scratch/stefan/7916117/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(F)=C2)CC1) `REAL250005035647.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035647 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(F)=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 53, 131, 131, 131, 131, 131, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 11, 48, 48, 53, 53, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 33, 11, 12, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 314 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035647 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(F)=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 19, 8, 1, 1, 1, 1, 1, 1, 1, 54, 131, 201, 201, 201, 201, 201, 201, 131, 131, 54, 19, 19, 8, 8, 201, 201, 201, 201, 131, 131, 131, 131] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 536 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: REAL250005035647 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC(F)=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 31, 31, 102, 107, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 102, 102, 107, 107, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 560 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035647 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035647 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035647/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035647 Building REAL250005035648 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035648' /scratch/stefan/7916117/working/building/REAL250005035648 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035648 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035648/0 /scratch/stefan/7916117/working/building/REAL250005035648 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/208 `/scratch/stefan/7916117/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1CC) `REAL250005035648.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035648 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 85, 85, 54, 54, 54, 20, 8, 1, 1, 1, 1, 1, 1, 1, 84, 84, 85, 85, 201, 125, 125, 125, 125, 125, 53, 20, 20, 8, 8, 201, 201, 200, 201, 201] 201 rigid atoms, others: [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, 33, 34]) total number of confs: 975 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035648 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 31, 37, 84, 84, 84, 84, 84, 1, 1, 1, 1, 5, 2, 2, 2, 2, 2, 9, 31, 31, 37, 37, 5, 5, 6, 6, 6] 201 rigid atoms, others: [1, 2, 3, 4, 15, 16, 17, 18] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035648 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035648 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035648/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035648 Building REAL250005035649 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035649' /scratch/stefan/7916117/working/building/REAL250005035649 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035649 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035649/0 /scratch/stefan/7916117/working/building/REAL250005035649 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/209 `/scratch/stefan/7916117/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=NC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035649.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035649 none CCC1=NC=NC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 197, 197, 197, 128, 197, 197, 67, 67, 67, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 67, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 728 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035649 none CCC1=NC=NC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 56, 64, 197, 197, 197, 197, 197, 6, 6, 6, 6, 6, 1, 1, 10, 56, 56, 64, 64] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 24, 25] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035649 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035649 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035649/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035649 Building REAL250005035650 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035650' /scratch/stefan/7916117/working/building/REAL250005035650 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035650 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035650/0 /scratch/stefan/7916117/working/building/REAL250005035650 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/210 `/scratch/stefan/7916117/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCCC1=NC(=O)O[N-]1)N1CCCC1=O) `REAL250005035650.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035650 none CCC(C(=O)NCCC1=NC(=O)O[N-]1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 18, 18, 18, 81, 93, 195, 195, 195, 195, 195, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 6, 18, 81, 81, 93, 93, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 35, 36, 34, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 548 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: REAL250005035650 none CCC(C(=O)NCCC1=NC(=O)O[N-]1)N1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 175, 70, 70, 70, 23, 8, 1, 1, 1, 1, 1, 1, 1, 175, 195, 195, 195, 195, 195, 191, 191, 191, 191, 191, 175, 70, 23, 23, 8, 8, 195, 195, 195, 195, 195, 195] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 812 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035650 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035650 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035650/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035650 Building REAL250005035651 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035651' /scratch/stefan/7916117/working/building/REAL250005035651 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035651 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035651/0 /scratch/stefan/7916117/working/building/REAL250005035651 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/211 `/scratch/stefan/7916117/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1) `REAL250005035651.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035651 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 30, 103, 110, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 29, 103, 103, 110, 110, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 579 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035651 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 55, 55, 55, 19, 8, 1, 1, 1, 1, 1, 1, 1, 133, 201, 201, 201, 201, 201, 201, 133, 133, 133, 133, 55, 19, 19, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 644 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035651 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035651 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035651/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035651 Building REAL250005035652 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035652' /scratch/stefan/7916117/working/building/REAL250005035652 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035652 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035652/0 /scratch/stefan/7916117/working/building/REAL250005035652 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/212 `/scratch/stefan/7916117/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC1CCCC1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035652.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035652 none CCC(CC1CCCC1)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 119, 51, 119, 165, 201, 201, 201, 201, 51, 51, 19, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 119, 165, 165, 201, 201, 201, 201, 201, 201, 201, 201, 201, 51, 19, 19, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1026 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035652 none CCC(CC1CCCC1)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 9, 5, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 86, 96, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 86, 86, 96, 96] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 35, 36, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035652 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035652 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035652/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035652 Building REAL250005035653 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035653' /scratch/stefan/7916117/working/building/REAL250005035653 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035653 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035653/0 /scratch/stefan/7916117/working/building/REAL250005035653 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/213 `/scratch/stefan/7916117/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C) `REAL250005035653.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035653 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 108, 108, 108, 24, 8, 1, 1, 1, 1, 1, 1, 1, 176, 176, 177, 177, 177, 177, 177, 107, 24, 24, 8, 8, 177, 177, 177] 177 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 423 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: REAL250005035653 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 67, 100, 176, 176, 176, 176, 176, 1, 1, 1, 1, 2, 2, 2, 11, 67, 67, 100, 100, 2, 2, 2] 177 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 549 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035653 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035653 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035653/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035653 Building REAL250005035654 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035654' /scratch/stefan/7916117/working/building/REAL250005035654 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035654 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035654/0 /scratch/stefan/7916117/working/building/REAL250005035654 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/214 `/scratch/stefan/7916117/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CS1) `REAL250005035654.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035654 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 45, 45, 45, 120, 126, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 11, 11, 11, 11, 45, 120, 120, 126, 126, 1, 1, 1] 201 rigid atoms, others: [1, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005035654 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [153, 54, 54, 54, 19, 8, 1, 1, 1, 1, 1, 1, 1, 153, 201, 201, 201, 201, 153, 153, 153, 153, 54, 19, 19, 8, 8, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 674 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035654 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035654 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035654/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035654 Building REAL250005035655 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035655' /scratch/stefan/7916117/working/building/REAL250005035655 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035655 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035655/0 /scratch/stefan/7916117/working/building/REAL250005035655 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/215 `/scratch/stefan/7916117/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2F)CC1) `REAL250005035655.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035655 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 61, 70, 154, 154, 154, 154, 154, 1, 1, 5, 5, 2, 5, 5, 5, 1, 1, 11, 61, 61, 70, 70, 5, 5, 3, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 33, 11, 12, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035655 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 20, 8, 1, 1, 1, 1, 1, 1, 1, 50, 154, 201, 201, 201, 201, 201, 201, 154, 154, 50, 20, 20, 8, 8, 201, 201, 201, 201, 154, 154, 154, 154] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035655 none O=C(NCCC1=NC(=O)O[N-]1)C1(C2=CC=CC=C2F)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 26, 26, 102, 112, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 102, 102, 112, 112, 1, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 567 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035655 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035655 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035655/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035655 Building REAL250005035656 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035656' /scratch/stefan/7916117/working/building/REAL250005035656 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035656 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035656/0 /scratch/stefan/7916117/working/building/REAL250005035656 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/216 `/scratch/stefan/7916117/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1[N-]C(C(=O)NCCC2=NC(=O)O[N-]2)=CC1=O) `REAL250005035656.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035656 none CCN1[N-]C(C(=O)NCCC2=NC(=O)O[N-]2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 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: [83, 63, 63, 63, 43, 43, 43, 10, 8, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 83, 84, 84, 84, 84, 42, 10, 10, 8, 8, 63] 84 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL250005035656 none CCN1[N-]C(C(=O)NCCC2=NC(=O)O[N-]2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 12, 12, 12, 35, 36, 63, 63, 63, 63, 63, 1, 1, 1, 8, 8, 8, 7, 7, 12, 34, 34, 36, 36, 1] 84 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 29] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035656 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035656 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035656/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035656 Building REAL250005035657 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035657' /scratch/stefan/7916117/working/building/REAL250005035657 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035657 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035657/0 /scratch/stefan/7916117/working/building/REAL250005035657 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/217 `/scratch/stefan/7916117/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCC(CC)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035657.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035657 none CCCCCCC(CC)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 185, 146, 116, 106, 75, 34, 75, 81, 34, 34, 8, 8, 1, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 185, 185, 146, 146, 116, 116, 106, 106, 75, 90, 90, 90, 90, 90, 33, 9, 9, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 1030 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035657 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035657 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035657/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035657 Building REAL250005035658 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035658' /scratch/stefan/7916117/working/building/REAL250005035658 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035658 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035658/0 /scratch/stefan/7916117/working/building/REAL250005035658 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/218 `/scratch/stefan/7916117/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=N1) `REAL250005035658.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035658 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [13, 1, 13, 13, 57, 67, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 1, 13, 57, 57, 67, 67, 1, 1, 1] 113 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035658 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [75, 75, 22, 8, 1, 1, 1, 1, 1, 1, 1, 75, 113, 113, 113, 113, 113, 113, 75, 22, 22, 8, 8, 113, 113, 113] 113 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035658 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035658 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035658/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035658 Building REAL250005035659 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035659' /scratch/stefan/7916117/working/building/REAL250005035659 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035659 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035659/0 /scratch/stefan/7916117/working/building/REAL250005035659 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/219 `/scratch/stefan/7916117/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=CO2)S1) `REAL250005035659.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035659 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=CO2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 12, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 1, 12, 12, 62, 77, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 1, 1, 12, 62, 62, 77, 77, 1, 1, 1] 137 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 402 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035659 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=CO2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 12, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [77, 77, 23, 8, 1, 1, 1, 1, 1, 1, 1, 77, 137, 137, 137, 137, 137, 137, 137, 77, 23, 24, 8, 8, 137, 137, 137] 137 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035659 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035659 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035659/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035659 Building REAL250005035660 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035660' /scratch/stefan/7916117/working/building/REAL250005035660 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035660 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035660/0 /scratch/stefan/7916117/working/building/REAL250005035660 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/220 `/scratch/stefan/7916117/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1(O)CCCC1)NCCC1=NC(=O)O[N-]1) `REAL250005035660.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035660 none O=C(CC1(O)CCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 186, 201, 201, 201, 201, 201, 22, 8, 1, 1, 1, 1, 1, 1, 1, 186, 186, 603, 201, 201, 201, 201, 201, 201, 201, 201, 84, 23, 23, 8, 8] 603 rigid atoms, others: [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]) total number of confs: 1388 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: REAL250005035660 none O=C(CC1(O)CCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 1, 1, 1, 1, 1, 1, 1, 24, 24, 89, 110, 201, 201, 201, 201, 201, 7, 7, 6, 1, 1, 1, 1, 1, 1, 1, 1, 24, 89, 89, 110, 110] 603 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31]) total number of confs: 598 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035660 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035660 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035660/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035660 Building REAL250005035661 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035661' /scratch/stefan/7916117/working/building/REAL250005035661 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035661 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035661/0 /scratch/stefan/7916117/working/building/REAL250005035661 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/221 `/scratch/stefan/7916117/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1=CC=CC=C1F)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035661.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035661 none CC(CC1=CC=CC=C1F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 1, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [107, 48, 107, 169, 201, 201, 201, 201, 201, 201, 48, 48, 19, 8, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 169, 169, 201, 201, 201, 201, 48, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035661 none CC(CC1=CC=CC=C1F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 1, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 15, 47, 47, 47, 118, 121, 201, 201, 201, 201, 201, 15, 15, 15, 15, 7, 7, 1, 1, 1, 1, 47, 118, 118, 121, 121] 201 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: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035661 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035661 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035661/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035661 Building REAL250005035662 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035662' /scratch/stefan/7916117/working/building/REAL250005035662 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035662 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035662/0 /scratch/stefan/7916117/working/building/REAL250005035662 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/222 `/scratch/stefan/7916117/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(C)C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035662.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035662 none CC1=CC=CC(C(C)C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 116, 53, 116, 53, 53, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 116, 116, 116, 116, 53, 19, 19, 8, 8, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL250005035662 none CC1=CC=CC(C(C)C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 8, 8, 33, 32, 33, 105, 113, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 8, 9, 9, 9, 32, 105, 105, 113, 113, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 23, 24, 25, 35] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035662 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035662 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035662/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035662 Building REAL250005035663 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035663' /scratch/stefan/7916117/working/building/REAL250005035663 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035663 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035663/0 /scratch/stefan/7916117/working/building/REAL250005035663 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/223 `/scratch/stefan/7916117/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC=C1) `REAL250005035663.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035663 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 37, 37, 37, 113, 121, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 11, 11, 11, 11, 37, 113, 113, 121, 121, 1, 1, 1] 201 rigid atoms, others: [1, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005035663 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CSC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [134, 55, 55, 55, 19, 8, 1, 1, 1, 1, 1, 1, 1, 134, 201, 201, 201, 201, 134, 134, 134, 134, 55, 19, 19, 8, 8, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 657 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035663 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035663 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035663/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035663 Building REAL250005035664 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035664' /scratch/stefan/7916117/working/building/REAL250005035664 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035664 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035664/0 /scratch/stefan/7916117/working/building/REAL250005035664 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/224 `/scratch/stefan/7916117/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(Cl)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005035664.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035664 none CC1=NC=C(Cl)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 157, 157, 100, 100, 100, 24, 8, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 157, 100, 25, 25, 8, 8] 157 rigid atoms, others: [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]) 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: REAL250005035664 none CC1=NC=C(Cl)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 66, 157, 157, 157, 157, 157, 1, 2, 2, 2, 1, 7, 37, 37, 66, 66] 157 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 22] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035664 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035664 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035664/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035664 Building REAL250005035665 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035665' /scratch/stefan/7916117/working/building/REAL250005035665 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035665 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035665/0 /scratch/stefan/7916117/working/building/REAL250005035665 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/225 `/scratch/stefan/7916117/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(NC2CC2)=N1) `REAL250005035665.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035665 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(NC2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 8, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 23, 31, 96, 96, 96, 97, 97, 1, 1, 1, 1, 1, 2, 13, 13, 1, 6, 23, 23, 32, 32, 1, 2, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035665 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(NC2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 8, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 20, 8, 1, 1, 1, 1, 1, 1, 1, 63, 97, 97, 96, 96, 130, 201, 201, 96, 62, 20, 20, 8, 8, 97, 130, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 679 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035665 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(NC2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 8, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 13, 40, 40, 94, 115, 201, 201, 201, 201, 201, 13, 13, 13, 8, 1, 1, 1, 1, 13, 40, 94, 94, 115, 115, 13, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 635 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035665 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035665 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035665/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035665 Building REAL250005035666 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035666' /scratch/stefan/7916117/working/building/REAL250005035666 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035666 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035666/0 /scratch/stefan/7916117/working/building/REAL250005035666 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/226 `/scratch/stefan/7916117/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005035666.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035666 none CSC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 16, 16, 16, 59, 70, 163, 163, 163, 163, 163, 1, 1, 1, 1, 1, 1, 11, 11, 11, 4, 16, 59, 59, 70, 70, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005035666 none CSC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 134, 46, 46, 46, 17, 8, 1, 1, 1, 1, 1, 1, 1, 134, 163, 163, 134, 163, 163, 168, 168, 168, 134, 45, 17, 17, 8, 8, 163, 163, 134, 163, 163] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035666 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035666 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035666/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035666 Building REAL250005035667 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035667' /scratch/stefan/7916117/working/building/REAL250005035667 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035667 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035667/0 /scratch/stefan/7916117/working/building/REAL250005035667 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/227 `/scratch/stefan/7916117/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=CO1) `REAL250005035667.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035667 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 193, 193, 116, 116, 116, 24, 8, 1, 1, 1, 1, 1, 1, 1, 193, 193, 193, 201, 201, 201, 201, 201, 116, 24, 24, 8, 8, 193] 201 rigid atoms, others: [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]) total number of confs: 517 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035667 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [6, 1, 1, 1, 1, 6, 6, 6, 36, 64, 193, 193, 193, 193, 193, 1, 1, 1, 6, 6, 6, 6, 6, 6, 36, 36, 64, 64, 1] 201 rigid atoms, others: [1, 2, 3, 4, 15, 16, 17, 28] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035667 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035667 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035667/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035667 Building REAL250005035668 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035668' /scratch/stefan/7916117/working/building/REAL250005035668 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035668 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035668/0 /scratch/stefan/7916117/working/building/REAL250005035668 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/228 `/scratch/stefan/7916117/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC=CN2C=CN=C12) `REAL250005035668.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035668 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC=CN2C=CN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [12, 1, 12, 12, 70, 110, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 70, 70, 110, 110, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 607 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035668 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC=CN2C=CN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 22, 8, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 201, 201, 201, 82, 22, 22, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035668 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035668 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035668/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035668 Building REAL250005035669 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035669' /scratch/stefan/7916117/working/building/REAL250005035669 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035669 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035669/0 /scratch/stefan/7916117/working/building/REAL250005035669 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/229 `/scratch/stefan/7916117/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(O)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035669.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035669 none CC1=CC(O)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 150, 150, 150, 64, 64, 64, 22, 8, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 300, 150, 63, 22, 22, 8, 8, 150] 300 rigid atoms, others: [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]) total number of confs: 644 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035669 none CC1=CC(O)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 38, 63, 150, 150, 150, 150, 150, 1, 2, 2, 2, 1, 2, 1, 7, 38, 38, 63, 63, 1] 300 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 22, 24, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 25, 26, 27, 28, 29]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035669 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035669 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035669/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035669 Building REAL250005035670 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035670' /scratch/stefan/7916117/working/building/REAL250005035670 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035670 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035670/0 /scratch/stefan/7916117/working/building/REAL250005035670 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/230 `/scratch/stefan/7916117/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC2COCC(C1)C2=O) `REAL250005035670.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035670 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2COCC(C1)C2=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 38, 52, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 38, 38, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 116 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 308 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: REAL250005035670 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2COCC(C1)C2=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 21, 8, 1, 1, 1, 1, 1, 1, 1, 72, 117, 117, 117, 117, 117, 117, 117, 117, 117, 72, 22, 22, 8, 8, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117] 117 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 406 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035670 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035670 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035670/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035670 Building REAL250005035671 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035671' /scratch/stefan/7916117/working/building/REAL250005035671 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035671 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035671/0 /scratch/stefan/7916117/working/building/REAL250005035671 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/231 `/scratch/stefan/7916117/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCSCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035671.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035671 none CCCCSCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 197, 129, 73, 73, 28, 28, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 197, 197, 79, 79, 79, 79, 27, 9, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 795 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035671 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035671 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035671/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035671 Building REAL250005035672 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035672' /scratch/stefan/7916117/working/building/REAL250005035672 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035672 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035672/0 /scratch/stefan/7916117/working/building/REAL250005035672 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/232 `/scratch/stefan/7916117/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=CN=C2)=C1) `REAL250005035672.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035672 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=CN=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 35, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 5, 29, 29, 35, 35, 1, 1, 1, 7, 7, 7, 1] 201 rigid atoms, others: [1, 33, 11, 12, 13, 14, 15, 16, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32]) 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: REAL250005035672 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=CN=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 51, 19, 8, 1, 1, 1, 1, 1, 1, 1, 51, 113, 113, 113, 113, 113, 201, 201, 201, 201, 113, 51, 19, 19, 8, 8, 113, 113, 113, 201, 201, 201, 113] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL250005035672 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(N2C=CN=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 23, 23, 90, 96, 201, 201, 201, 201, 201, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 23, 90, 90, 96, 96, 6, 7, 7, 1, 1, 1, 7] 201 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 519 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035672 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035672 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035672/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035672 Building REAL250005035673 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035673' /scratch/stefan/7916117/working/building/REAL250005035673 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035673 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035673/0 /scratch/stefan/7916117/working/building/REAL250005035673 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/233 `/scratch/stefan/7916117/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C)=NC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035673.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035673 none CCC1=NC(C)=NC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 191, 191, 191, 69, 69, 191, 191, 69, 69, 69, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 191, 191, 191, 191, 69, 19, 19, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035673 none CCC1=NC(C)=NC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 55, 64, 191, 191, 191, 191, 191, 6, 6, 6, 6, 6, 2, 2, 2, 1, 10, 55, 55, 64, 64] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035673 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035673 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035673/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035673 Building REAL250005035674 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035674' /scratch/stefan/7916117/working/building/REAL250005035674 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035674 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035674/0 /scratch/stefan/7916117/working/building/REAL250005035674 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/234 `/scratch/stefan/7916117/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(F)=CC=C2O1) `REAL250005035674.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035674 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(F)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [10, 1, 10, 10, 49, 70, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 49, 49, 70, 70, 1, 1, 1, 1] 109 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) 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: REAL250005035674 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC(F)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [75, 75, 22, 8, 1, 1, 1, 1, 1, 1, 1, 75, 109, 109, 109, 109, 109, 109, 109, 109, 109, 75, 22, 22, 8, 8, 109, 109, 109, 109] 109 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035674 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035674 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035674/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035674 Building REAL250005035675 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035675' /scratch/stefan/7916117/working/building/REAL250005035675 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035675 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035675/0 /scratch/stefan/7916117/working/building/REAL250005035675 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/235 `/scratch/stefan/7916117/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1=CC=CN=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035675.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035675 none CC(OC1=CC=CN=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [84, 35, 89, 119, 201, 201, 201, 201, 201, 35, 35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 89, 89, 84, 89, 201, 201, 201, 201, 34, 9, 9, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 528 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035675 none CC(OC1=CC=CN=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 1, 1, 1, 1, 1, 1, 1, 24, 65, 65, 65, 117, 117, 201, 201, 201, 201, 201, 24, 24, 24, 24, 1, 1, 1, 1, 65, 117, 117, 117, 117] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32]) total number of confs: 581 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035675 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035675 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035675/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035675 Building REAL250005035676 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035676' /scratch/stefan/7916117/working/building/REAL250005035676 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035676 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035676/0 /scratch/stefan/7916117/working/building/REAL250005035676 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/236 `/scratch/stefan/7916117/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035676.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035676 none CSCCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 125, 125, 115, 103, 43, 43, 43, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 125, 125, 125, 125, 125, 125, 103, 103, 43, 17, 17, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035676 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035676 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035676/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035676 Building REAL250005035677 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035677' /scratch/stefan/7916117/working/building/REAL250005035677 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035677 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035677/0 /scratch/stefan/7916117/working/building/REAL250005035677 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/237 `/scratch/stefan/7916117/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1) `REAL250005035677.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035677 none CCOC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 193, 171, 171, 171, 58, 58, 58, 19, 8, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 201, 201, 201, 201, 201, 171, 58, 19, 19, 8, 8, 171, 171] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 443 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035677 none CCOC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 3, 1, 1, 1, 1, 1, 5, 5, 5, 29, 38, 171, 171, 171, 171, 171, 1, 1, 1, 18, 18, 18, 17, 17, 1, 5, 29, 29, 38, 38, 1, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 17, 18, 19, 25, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035677 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035677 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035677/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035677 Building REAL250005035678 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035678' /scratch/stefan/7916117/working/building/REAL250005035678 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035678 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035678/0 /scratch/stefan/7916117/working/building/REAL250005035678 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/238 `/scratch/stefan/7916117/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1CC(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035678.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035678 none CC1=NOC(C)=C1CC(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 145, 103, 38, 103, 38, 38, 16, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 145, 145, 103, 103, 103, 103, 38, 16, 16, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 748 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035678 none CC1=NOC(C)=C1CC(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 42, 42, 42, 118, 120, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 6, 6, 13, 13, 13, 13, 42, 118, 118, 120, 120] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035678 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035678 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035678/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035678 Building REAL250005035679 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035679' /scratch/stefan/7916117/working/building/REAL250005035679 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035679 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035679/0 /scratch/stefan/7916117/working/building/REAL250005035679 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/239 `/scratch/stefan/7916117/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC=C2C=C1) `REAL250005035679.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035679 none CC1=NC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 184, 97, 97, 97, 23, 8, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 184, 184, 184, 184, 97, 23, 23, 8, 8, 184, 184, 184, 184, 184] 184 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL250005035679 none CC1=NC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 70, 96, 184, 184, 184, 184, 184, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 70, 70, 96, 96, 1, 1, 1, 1, 1] 184 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 34, 16, 17, 18, 19, 20, 21, 33, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035679 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035679 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035679/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035679 Building REAL250005035680 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035680' /scratch/stefan/7916117/working/building/REAL250005035680 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035680 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035680/0 /scratch/stefan/7916117/working/building/REAL250005035680 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/240 `/scratch/stefan/7916117/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C2C=CC=CN12) `REAL250005035680.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035680 none CC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C2C=CC=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 185, 93, 93, 93, 22, 8, 1, 1, 1, 1, 1, 1, 1, 185, 185, 185, 185, 185, 185, 185, 185, 185, 92, 22, 22, 8, 8, 184, 184, 185, 185] 185 rigid atoms, others: [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]) total number of confs: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035680 none CC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C2C=CC=CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 61, 85, 184, 184, 184, 184, 184, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 61, 61, 86, 86, 1, 1, 1, 1] 185 rigid atoms, others: [0, 1, 2, 3, 4, 32, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 509 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035680 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035680 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035680/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035680 Building REAL250005035681 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035681' /scratch/stefan/7916117/working/building/REAL250005035681 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035681 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035681/0 /scratch/stefan/7916117/working/building/REAL250005035681 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/241 `/scratch/stefan/7916117/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCOC1=CC=CN=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035681.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035681 none O=C(CCCOC1=CC=CN=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 85, 74, 118, 177, 201, 201, 201, 201, 201, 13, 7, 1, 1, 1, 1, 1, 1, 1, 85, 85, 100, 100, 104, 104, 201, 201, 201, 201, 35, 13, 13, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 763 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035681 none O=C(CCCOC1=CC=CN=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 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: [58, 33, 23, 12, 6, 1, 1, 1, 1, 1, 1, 1, 58, 58, 122, 122, 201, 201, 201, 201, 201, 33, 33, 23, 23, 12, 12, 1, 1, 1, 1, 58, 122, 122, 122, 122] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035681 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035681 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035681/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035681 Building REAL250005035682 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035682' /scratch/stefan/7916117/working/building/REAL250005035682 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035682 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035682/0 /scratch/stefan/7916117/working/building/REAL250005035682 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/242 `/scratch/stefan/7916117/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005035682.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035682 none CC1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 80, 80, 80, 24, 8, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 121, 121, 121, 121, 121, 121, 121, 121, 80, 24, 24, 8, 8, 121, 121, 121, 121] 121 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035682 none CC1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 35, 49, 121, 121, 121, 121, 121, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 35, 35, 49, 49, 1, 1, 1, 1] 121 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 34, 33, 16, 17, 35, 21, 22, 23, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035682 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035682 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035682/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035682 Building REAL250005035683 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035683' /scratch/stefan/7916117/working/building/REAL250005035683 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035683 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035683/0 /scratch/stefan/7916117/working/building/REAL250005035683 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/243 `/scratch/stefan/7916117/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035683.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035683 none COC1=CC=C(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 134, 134, 201, 201, 134, 71, 134, 71, 71, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 71, 19, 19, 8, 8, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 811 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035683 none COC1=CC=C(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 11, 11, 41, 41, 41, 107, 116, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 41, 107, 107, 116, 116, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 19, 20, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 603 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035683 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035683 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035683/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035683 Building REAL250005035684 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035684' /scratch/stefan/7916117/working/building/REAL250005035684 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035684 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035684/0 /scratch/stefan/7916117/working/building/REAL250005035684 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/244 `/scratch/stefan/7916117/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1) `REAL250005035684.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035684 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 151, 151, 151, 151, 90, 90, 90, 24, 8, 1, 1, 1, 1, 1, 1, 1, 151, 151, 167, 167, 167, 151, 151, 90, 24, 24, 8, 8] 167 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 401 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035684 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 3, 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: [2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 67, 97, 151, 151, 151, 151, 151, 1, 1, 2, 2, 2, 1, 1, 12, 67, 67, 97, 97] 167 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 22, 23] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035684 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035684 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035684/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035684 Building REAL250005035685 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035685' /scratch/stefan/7916117/working/building/REAL250005035685 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035685 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035685/0 /scratch/stefan/7916117/working/building/REAL250005035685 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/245 `/scratch/stefan/7916117/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC=C1F) `REAL250005035685.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035685 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 71, 110, 197, 197, 197, 197, 197, 1, 1, 1, 1, 1, 1, 1, 12, 71, 71, 110, 110, 1, 1, 1] 197 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) 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: REAL250005035685 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 24, 8, 1, 1, 1, 1, 1, 1, 1, 98, 197, 197, 197, 197, 197, 197, 98, 24, 24, 8, 8, 197, 197, 197] 197 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035685 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035685 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035685/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035685 Building REAL250005035686 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035686' /scratch/stefan/7916117/working/building/REAL250005035686 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035686 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035686/0 /scratch/stefan/7916117/working/building/REAL250005035686 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/246 `/scratch/stefan/7916117/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1) `REAL250005035686.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035686 none CC(C)CCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 188, 113, 113, 113, 76, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 112, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 191, 191, 113, 75, 24, 24, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 771 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035686 none CC(C)CCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [11, 11, 11, 8, 1, 1, 1, 1, 1, 6, 7, 7, 18, 27, 113, 113, 112, 113, 113, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 1, 7, 17, 17, 27, 27] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 19, 20] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035686 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035686 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035686/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035686 Building REAL250005035687 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035687' /scratch/stefan/7916117/working/building/REAL250005035687 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035687 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035687/0 /scratch/stefan/7916117/working/building/REAL250005035687 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/247 `/scratch/stefan/7916117/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035687.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035687 none CCC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 95, 95, 201, 201, 95, 43, 43, 43, 17, 8, 1, 1, 1, 1, 1, 1, 1, 197, 201, 201, 201, 201, 201, 201, 201, 201, 95, 95, 43, 17, 17, 8, 8, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 1360 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035687 none CCC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 7, 17, 17, 17, 76, 84, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 7, 17, 76, 76, 84, 84, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 18, 19, 23, 24, 25, 26, 35] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035687 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035687 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035687/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035687 Building REAL250005035688 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035688' /scratch/stefan/7916117/working/building/REAL250005035688 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035688 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035688/0 /scratch/stefan/7916117/working/building/REAL250005035688 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/248 `/scratch/stefan/7916117/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC1=NC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035688.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035688 none CC(C)NC1=NC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 186, 186, 186, 186, 186, 186, 61, 61, 61, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 186, 186, 186, 61, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 428 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035688 none CC(C)NC1=NC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [11, 4, 11, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 45, 55, 186, 186, 186, 186, 186, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 10, 45, 45, 55, 55] 201 rigid atoms, others: [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, 32, 33, 34, 35, 36]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035688 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035688 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035688/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035688 Building REAL250005035689 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035689' /scratch/stefan/7916117/working/building/REAL250005035689 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035689 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035689/0 /scratch/stefan/7916117/working/building/REAL250005035689 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/249 `/scratch/stefan/7916117/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC2=CC=CC=C21) `REAL250005035689.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035689 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 67, 105, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 13, 67, 67, 105, 105, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 580 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: REAL250005035689 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 92, 201, 201, 201, 201, 201, 201, 201, 92, 24, 25, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 592 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035689 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035689 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035689/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035689 Building REAL250005035690 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035690' /scratch/stefan/7916117/working/building/REAL250005035690 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035690 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035690/0 /scratch/stefan/7916117/working/building/REAL250005035690 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/250 `/scratch/stefan/7916117/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCCOCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035690.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035690 none CCCCCCCCOCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 105, 87, 54, 15, 15, 15, 7, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 105, 54, 54, 15, 7, 7, 5, 5] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 865 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035690 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035690 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035690/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035690 Building REAL250005035691 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035691' /scratch/stefan/7916117/working/building/REAL250005035691 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035691 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035691/0 /scratch/stefan/7916117/working/building/REAL250005035691 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/251 `/scratch/stefan/7916117/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCCCCC1) `REAL250005035691.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035691 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 60, 95, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 11, 60, 60, 95, 95, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 567 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: REAL250005035691 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 24, 8, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 201, 201, 201, 101, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 613 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035691 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035691 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035691/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035691 Building REAL250005035692 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035692' /scratch/stefan/7916117/working/building/REAL250005035692 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035692 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035692/0 /scratch/stefan/7916117/working/building/REAL250005035692 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/252 `/scratch/stefan/7916117/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CO1) `REAL250005035692.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035692 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 48, 48, 48, 134, 135, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 10, 10, 10, 10, 48, 134, 134, 135, 135, 1, 1, 1] 201 rigid atoms, others: [1, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 626 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035692 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 51, 51, 51, 19, 8, 1, 1, 1, 1, 1, 1, 1, 159, 201, 201, 201, 201, 159, 159, 159, 159, 51, 19, 19, 8, 8, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 679 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035692 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035692 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035692/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035692 Building REAL250005035693 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035693' /scratch/stefan/7916117/working/building/REAL250005035693 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035693 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035693/0 /scratch/stefan/7916117/working/building/REAL250005035693 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/253 `/scratch/stefan/7916117/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035693.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035693 none CC1=CC(F)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 147, 147, 55, 55, 55, 20, 8, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 147, 55, 20, 20, 8, 8, 147] 147 rigid atoms, others: [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]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035693 none CC1=CC(F)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 63, 147, 147, 147, 147, 147, 1, 2, 2, 2, 1, 1, 7, 39, 39, 63, 63, 1] 147 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 22, 23, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035693 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035693 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035693/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035693 Building REAL250005035694 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035694' /scratch/stefan/7916117/working/building/REAL250005035694 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035694 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035694/0 /scratch/stefan/7916117/working/building/REAL250005035694 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/254 `/scratch/stefan/7916117/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035694.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035694 none COC(=O)C1CCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 98, 201, 98, 98, 98, 98, 54, 54, 54, 17, 8, 1, 1, 1, 1, 1, 1, 1, 98, 201, 201, 201, 98, 98, 98, 98, 98, 98, 98, 98, 53, 17, 17, 8, 8, 98, 98] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 645 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035694 none COC(=O)C1CCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 24, 35, 98, 98, 98, 98, 98, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 24, 24, 35, 35, 1, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 38, 37, 20, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 3, 36, 33, 35, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035694 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035694 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035694/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035694 Building REAL250005035695 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035695' /scratch/stefan/7916117/working/building/REAL250005035695 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035695 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035695/0 /scratch/stefan/7916117/working/building/REAL250005035695 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/255 `/scratch/stefan/7916117/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(CCC(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005035695.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035695 none CC1CCC(CCC(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 156, 144, 55, 55, 55, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 144, 144, 55, 19, 19, 8, 8] 201 rigid atoms, others: [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, 36]) total number of confs: 960 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035695 none CC1CCC(CCC(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 13, 42, 42, 42, 101, 104, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 13, 13, 42, 101, 101, 104, 104] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 22, 23, 24, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035695 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035695 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035695/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035695 Building REAL250005035696 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035696' /scratch/stefan/7916117/working/building/REAL250005035696 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035696 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035696/0 /scratch/stefan/7916117/working/building/REAL250005035696 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/256 `/scratch/stefan/7916117/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NO1) `REAL250005035696.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035696 none COCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 200, 112, 112, 112, 73, 73, 73, 21, 7, 1, 1, 1, 1, 1, 1, 1, 112, 112, 201, 201, 201, 200, 200, 112, 72, 22, 22, 7, 7] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 742 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035696 none COCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [27, 8, 1, 1, 1, 1, 1, 7, 7, 7, 26, 35, 112, 112, 112, 112, 112, 1, 1, 28, 27, 27, 8, 8, 1, 7, 26, 26, 35, 35] 201 rigid atoms, others: [2, 3, 4, 5, 6, 17, 18, 24] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035696 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035696 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035696/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035696 Building REAL250005035697 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035697' /scratch/stefan/7916117/working/building/REAL250005035697 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035697 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035697/0 /scratch/stefan/7916117/working/building/REAL250005035697 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/257 `/scratch/stefan/7916117/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC=C1O) `REAL250005035697.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035697 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 270 conformations in input total number of sets (complete confs): 270 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 42, 52, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 1, 1, 9, 42, 42, 52, 52, 1, 1, 1, 2] 270 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 27]) total number of confs: 324 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035697 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 270 conformations in input total number of sets (complete confs): 270 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 19, 8, 1, 1, 1, 1, 1, 1, 1, 78, 135, 135, 135, 135, 135, 135, 135, 78, 20, 20, 8, 8, 135, 134, 135, 270] 270 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 610 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035697 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035697/1 /scratch/stefan/7916117/working/building/REAL250005035697 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/258 `/scratch/stefan/7916117/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC=C1[O-]) `REAL250005035697.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035697 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 14, 14, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 1, 1, 1] 26 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005035697 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [18, 18, 8, 8, 1, 1, 1, 1, 1, 1, 1, 18, 26, 26, 26, 26, 26, 26, 26, 18, 8, 8, 8, 8, 26, 26, 26] 26 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035697 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035697 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035697/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035697/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035697 Building REAL250005035698 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035698' /scratch/stefan/7916117/working/building/REAL250005035698 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035698 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035698/0 /scratch/stefan/7916117/working/building/REAL250005035698 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/259 `/scratch/stefan/7916117/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1O) `REAL250005035698.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035698 none CCC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 112, 112, 95, 111, 111, 72, 72, 72, 22, 8, 1, 1, 1, 1, 1, 1, 1, 112, 112, 201, 201, 201, 201, 201, 112, 111, 111, 71, 23, 23, 8, 8, 224] 402 rigid atoms, others: [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]) total number of confs: 1114 number of broken/clashed sets: 188 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035698 none CCC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 46, 111, 111, 111, 112, 112, 1, 1, 6, 6, 6, 6, 6, 1, 1, 1, 7, 33, 33, 47, 47, 2] 402 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 18, 19, 25, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 306 number of broken/clashed sets: 188 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035698 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035698 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035698/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035698 Building REAL250005035699 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035699' /scratch/stefan/7916117/working/building/REAL250005035699 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035699 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035699/0 /scratch/stefan/7916117/working/building/REAL250005035699 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/260 `/scratch/stefan/7916117/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1F) `REAL250005035699.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035699 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 104, 110, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 104, 104, 110, 110, 1, 1, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL250005035699 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 62, 62, 63, 20, 8, 1, 1, 1, 1, 1, 1, 1, 164, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 62, 20, 20, 8, 8, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 698 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035699 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035699 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035699/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035699 Building REAL250005035700 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035700' /scratch/stefan/7916117/working/building/REAL250005035700 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035700 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035700/0 /scratch/stefan/7916117/working/building/REAL250005035700 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/261 `/scratch/stefan/7916117/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005035700.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035700 none CC(C)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 201, 137, 137, 137, 137, 59, 59, 59, 21, 8, 1, 1, 1, 1, 1, 1, 1, 137, 137, 201, 201, 201, 201, 201, 201, 201, 199, 137, 137, 59, 21, 21, 8, 8, 137] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 538 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: REAL250005035700 none CC(C)NC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 22, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 36, 137, 137, 137, 137, 137, 1, 1, 22, 22, 22, 22, 22, 22, 22, 8, 1, 1, 5, 29, 29, 36, 36, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 19, 20, 36, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 344 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035700 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035700 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035700/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035700 Building REAL250005035701 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035701' /scratch/stefan/7916117/working/building/REAL250005035701 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035701 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035701/0 /scratch/stefan/7916117/working/building/REAL250005035701 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/262 `/scratch/stefan/7916117/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C(F)=C1) `REAL250005035701.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035701 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 109, 112, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 32, 109, 109, 112, 112, 1, 1, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 569 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035701 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 52, 52, 52, 19, 8, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 201, 201, 201, 201, 131, 131, 131, 131, 52, 19, 19, 8, 8, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 657 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035701 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035701 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035701/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035701 Building REAL250005035702 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035702' /scratch/stefan/7916117/working/building/REAL250005035702 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035702 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035702/0 /scratch/stefan/7916117/working/building/REAL250005035702 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/263 `/scratch/stefan/7916117/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005035702.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035702 none CCCC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 196, 99, 99, 99, 99, 61, 61, 61, 19, 8, 1, 1, 1, 1, 1, 1, 1, 99, 201, 201, 201, 201, 201, 197, 197, 99, 61, 19, 19, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035702 none CCCC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [12, 7, 1, 1, 1, 1, 1, 1, 6, 6, 6, 30, 34, 99, 99, 99, 99, 99, 1, 12, 12, 12, 12, 12, 7, 7, 1, 7, 30, 30, 34, 34] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 18, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035702 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035702 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035702/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035702 Building REAL250005035703 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035703' /scratch/stefan/7916117/working/building/REAL250005035703 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035703 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035703/0 /scratch/stefan/7916117/working/building/REAL250005035703 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/264 `/scratch/stefan/7916117/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=C1) `REAL250005035703.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035703 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 29, 100, 104, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 100, 100, 104, 104, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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: REAL250005035703 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 53, 53, 53, 19, 8, 1, 1, 1, 1, 1, 1, 1, 124, 201, 201, 201, 201, 201, 201, 124, 124, 124, 124, 53, 19, 19, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035703 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035703 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035703/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035703 Building REAL250005035704 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035704' /scratch/stefan/7916117/working/building/REAL250005035704 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035704 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035704/0 /scratch/stefan/7916117/working/building/REAL250005035704 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/265 `/scratch/stefan/7916117/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC=C1Cl) `REAL250005035704.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035704 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 41, 69, 163, 163, 163, 163, 163, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 69, 69, 1, 1, 1] 163 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 439 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035704 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 22, 8, 1, 1, 1, 1, 1, 1, 1, 109, 163, 163, 163, 163, 163, 163, 109, 22, 22, 8, 8, 163, 163, 163] 163 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035704 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035704 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035704/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035704 Building REAL250005035705 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035705' /scratch/stefan/7916117/working/building/REAL250005035705 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035705 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035705/0 /scratch/stefan/7916117/working/building/REAL250005035705 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/266 `/scratch/stefan/7916117/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C2C=CSC2=C1) `REAL250005035705.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035705 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C2C=CSC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 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: [7, 1, 7, 7, 36, 61, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 36, 36, 61, 61, 1, 1, 1, 1] 130 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035705 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C2C=CSC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 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: [62, 62, 22, 8, 1, 1, 1, 1, 1, 1, 1, 62, 130, 130, 130, 130, 130, 130, 130, 130, 61, 22, 22, 8, 8, 130, 130, 130, 130] 130 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035705 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035705 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035705/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035705 Building REAL250005035706 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035706' /scratch/stefan/7916117/working/building/REAL250005035706 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035706 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035706/0 /scratch/stefan/7916117/working/building/REAL250005035706 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/267 `/scratch/stefan/7916117/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1CCOCC1)NCCC1=NC(=O)O[N-]1) `REAL250005035706.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035706 none O=C(CCC1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [46, 46, 46, 163, 160, 201, 201, 201, 201, 201, 15, 7, 1, 1, 1, 1, 1, 1, 1, 163, 163, 186, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 46, 15, 15, 7, 7] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 919 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035706 none O=C(CCC1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [34, 9, 5, 1, 1, 1, 1, 1, 1, 1, 34, 34, 110, 112, 201, 201, 201, 201, 201, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 110, 110, 112, 112] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 36, 33, 35, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035706 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035706 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035706/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035706 Building REAL250005035707 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035707' /scratch/stefan/7916117/working/building/REAL250005035707 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035707 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035707/0 /scratch/stefan/7916117/working/building/REAL250005035707 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/268 `/scratch/stefan/7916117/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(C)C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005035707.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035707 none CC1=CC=C(C(C)C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 130, 42, 130, 42, 42, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 130, 130, 130, 130, 42, 19, 19, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035707 none CC1=CC=C(C(C)C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [1, 1, 1, 1, 1, 1, 10, 10, 46, 46, 46, 121, 125, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 10, 11, 11, 11, 46, 121, 121, 125, 125] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 627 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035707 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035707 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035707/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035707 Building REAL250005035708 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035708' /scratch/stefan/7916117/working/building/REAL250005035708 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035708 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035708/0 /scratch/stefan/7916117/working/building/REAL250005035708 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/269 `/scratch/stefan/7916117/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C(F)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035708.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035708 none CCOC1=C(F)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 197, 176, 176, 176, 176, 176, 176, 176, 55, 55, 55, 17, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 176, 176, 176, 55, 17, 17, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 415 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035708 none CCOC1=C(F)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 62, 68, 176, 176, 176, 176, 176, 11, 11, 11, 10, 10, 1, 1, 1, 11, 62, 62, 68, 68] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035708 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035708 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035708/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035708 Building REAL250005035709 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035709' /scratch/stefan/7916117/working/building/REAL250005035709 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035709 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035709/0 /scratch/stefan/7916117/working/building/REAL250005035709 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/270 `/scratch/stefan/7916117/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1) `REAL250005035709.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035709 none CCNC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 175, 133, 133, 133, 82, 82, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 134, 134, 201, 201, 201, 201, 201, 175, 81, 24, 24, 8, 8, 134] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 669 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035709 none CCNC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 4, 1, 1, 1, 1, 1, 6, 6, 6, 25, 39, 133, 133, 133, 134, 134, 1, 1, 25, 25, 25, 24, 24, 4, 6, 25, 25, 40, 40, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 17, 18, 30] set([0, 1, 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: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035709 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035709 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035709/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035709 Building REAL250005035710 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035710' /scratch/stefan/7916117/working/building/REAL250005035710 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035710 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035710/0 /scratch/stefan/7916117/working/building/REAL250005035710 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/271 `/scratch/stefan/7916117/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1CCCC1)NCCC1=NC(=O)O[N-]1) `REAL250005035710.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035710 none O=C(CCCC1CCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 106, 116, 136, 201, 201, 201, 201, 15, 7, 1, 1, 1, 1, 1, 1, 1, 106, 106, 136, 136, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 201, 34, 15, 15, 7, 7] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 961 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035710 none O=C(CCCC1CCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 9, 4, 4, 1, 1, 1, 1, 1, 1, 39, 39, 107, 110, 201, 201, 201, 201, 201, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 107, 107, 110, 110] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38]) total number of confs: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035710 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035710 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035710/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035710 Building REAL250005035711 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035711' /scratch/stefan/7916117/working/building/REAL250005035711 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035711 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035711/0 /scratch/stefan/7916117/working/building/REAL250005035711 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/272 `/scratch/stefan/7916117/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCC1=CC=CC=C12) `REAL250005035711.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035711 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 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: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 7, 35, 56, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 35, 35, 56, 56, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 110 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035711 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCC1=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 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: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 23, 8, 1, 1, 1, 1, 1, 1, 1, 66, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 65, 23, 23, 8, 8, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110] 110 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035711 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035711 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035711/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035711 Building REAL250005035712 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035712' /scratch/stefan/7916117/working/building/REAL250005035712 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035712 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035712/0 /scratch/stefan/7916117/working/building/REAL250005035712 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/273 `/scratch/stefan/7916117/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C1CC1) `REAL250005035712.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035712 none CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', '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, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [130, 130, 130, 83, 83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 201, 201, 130, 130, 130, 82, 24, 24, 8, 8, 130, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 33]) total number of confs: 625 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035712 none CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', '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, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 11, 11, 11, 41, 56, 130, 130, 130, 130, 130, 1, 1, 1, 8, 8, 2, 2, 2, 11, 41, 41, 56, 56, 1, 8, 8, 8, 8, 8] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035712 none CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', '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, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [8, 8, 8, 8, 8, 40, 40, 40, 103, 114, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 8, 8, 8, 40, 103, 103, 114, 114, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 544 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035712 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035712 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035712/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035712 Building REAL250005035713 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035713' /scratch/stefan/7916117/working/building/REAL250005035713 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035713 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035713/0 /scratch/stefan/7916117/working/building/REAL250005035713 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/274 `/scratch/stefan/7916117/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC(F)=C2O1) `REAL250005035713.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035713 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 65, 90, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 64, 64, 90, 90, 1, 1, 1, 1] 155 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 474 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035713 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CC(F)=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 15, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [94, 94, 24, 8, 1, 1, 1, 1, 1, 1, 1, 94, 155, 155, 155, 155, 155, 155, 155, 155, 153, 94, 24, 24, 8, 8, 155, 155, 155, 155] 155 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035713 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035713 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035713/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035713 Building REAL250005035714 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035714' /scratch/stefan/7916117/working/building/REAL250005035714 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035714 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035714/0 /scratch/stefan/7916117/working/building/REAL250005035714 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/275 `/scratch/stefan/7916117/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC2=CC(F)=CC=C2O1) `REAL250005035714.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035714 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2=CC(F)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 64, 98, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 64, 64, 98, 98, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 573 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: REAL250005035714 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2=CC(F)=CC=C2O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 24, 8, 1, 1, 1, 1, 1, 1, 1, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 605 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035714 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035714 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035714/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035714 Building REAL250005035715 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035715' /scratch/stefan/7916117/working/building/REAL250005035715 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035715 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035715/0 /scratch/stefan/7916117/working/building/REAL250005035715 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/276 `/scratch/stefan/7916117/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCC(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035715.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035715 none CCCCCCC(C)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 144, 116, 104, 87, 35, 86, 35, 35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 187, 187, 148, 148, 114, 116, 108, 108, 88, 88, 86, 88, 34, 8, 8, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 966 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035715 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035715 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035715/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035715 Building REAL250005035716 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035716' /scratch/stefan/7916117/working/building/REAL250005035716 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035716 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035716/0 /scratch/stefan/7916117/working/building/REAL250005035716 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/277 `/scratch/stefan/7916117/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035716.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035716 none CS(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 172, 201, 172, 172, 172, 81, 81, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 172, 172, 201, 201, 201, 172, 172, 81, 24, 24, 8, 8, 172, 172] 201 rigid atoms, others: [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]) total number of confs: 519 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035716 none CS(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 6, 30, 56, 172, 172, 172, 172, 172, 1, 1, 7, 7, 7, 1, 1, 6, 30, 30, 56, 56, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 23, 24, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035716 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035716 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035716/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035716 Building REAL250005035717 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035717' /scratch/stefan/7916117/working/building/REAL250005035717 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005035717 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035717/0 /scratch/stefan/7916117/working/building/REAL250005035717 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/278 `/scratch/stefan/7916117/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035717.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035717 none CN1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 111, 111, 111, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 24, 24, 8, 8, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 613 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035717 none CN1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 13, 13, 13, 77, 115, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 13, 77, 77, 115, 115, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 17, 21, 22, 23, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 26, 27, 28, 29, 30]) total number of confs: 626 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035717 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035717/1 /scratch/stefan/7916117/working/building/REAL250005035717 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/279 `/scratch/stefan/7916117/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035717.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035717 none C[N@@H+]1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 114, 114, 71, 71, 71, 17, 9, 1, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 114, 114, 114, 114, 71, 17, 17, 9, 9, 114, 114] 114 rigid atoms, others: [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]) total number of confs: 372 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035717 none C[N@@H+]1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 57, 64, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 57, 57, 64, 64, 1, 1] 114 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035717 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `2' /scratch/stefan/7916117/working/building/REAL250005035717/2 /scratch/stefan/7916117/working/building/REAL250005035717 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 2 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/280 `/scratch/stefan/7916117/working/3D/280' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035717.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005035717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035717/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035717 none C[N@H+]1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 17, 17, 17, 12, 9, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 17, 12, 12, 9, 9, 19, 19] 19 rigid atoms, others: [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]) 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: REAL250005035717 none C[N@H+]1CCOC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 6, 6, 6, 12, 12, 19, 19, 19, 19, 19, 1, 2, 2, 2, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 1, 1] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 18, 32, 22, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 27, 28, 29, 30, 31]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035717 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035717 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035717/0.* 2: /scratch/stefan/7916117/working/building/REAL250005035717/2.* 1: /scratch/stefan/7916117/working/building/REAL250005035717/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035717 Building REAL250005035718 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035718' /scratch/stefan/7916117/working/building/REAL250005035718 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035718 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035718/0 /scratch/stefan/7916117/working/building/REAL250005035718 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/281 `/scratch/stefan/7916117/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005035718.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035718 none CC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 173, 173, 95, 95, 95, 24, 8, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 173, 173, 173, 95, 24, 24, 8, 8] 173 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 407 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: REAL250005035718 none CC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 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, 1, 11, 11, 11, 59, 99, 173, 173, 173, 173, 173, 1, 2, 2, 2, 2, 2, 2, 11, 59, 59, 99, 99] 173 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 544 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035718 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035718 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035718/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035718 Building REAL250005035719 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035719' /scratch/stefan/7916117/working/building/REAL250005035719 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035719 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035719/0 /scratch/stefan/7916117/working/building/REAL250005035719 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/282 `/scratch/stefan/7916117/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005035719.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035719 none CCNC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 186, 136, 136, 136, 136, 72, 72, 72, 23, 8, 1, 1, 1, 1, 1, 1, 1, 136, 201, 201, 201, 201, 201, 186, 136, 72, 23, 23, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035719 none CCNC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [23, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 34, 39, 136, 136, 136, 136, 136, 1, 23, 23, 23, 23, 23, 6, 1, 6, 34, 34, 39, 39] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 18, 25] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035719 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035719 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035719/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035719 Building REAL250005035720 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035720' /scratch/stefan/7916117/working/building/REAL250005035720 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035720 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035720/0 /scratch/stefan/7916117/working/building/REAL250005035720 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/283 `/scratch/stefan/7916117/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C(F)(F)F) `REAL250005035720.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035720 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 102, 102, 102, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 102, 24, 24, 8, 8] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 792 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035720 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035720 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035720/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035720 Building REAL250005035721 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035721' /scratch/stefan/7916117/working/building/REAL250005035721 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035721 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035721/0 /scratch/stefan/7916117/working/building/REAL250005035721 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/284 `/scratch/stefan/7916117/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1Cl) `REAL250005035721.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035721 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 41, 69, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 69, 69, 1, 1, 1] 151 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035721 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 22, 8, 1, 1, 1, 1, 1, 1, 1, 95, 151, 151, 151, 151, 151, 151, 151, 95, 22, 22, 8, 8, 151, 151, 151] 151 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035721 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035721 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035721/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035721 Building REAL250005035722 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035722' /scratch/stefan/7916117/working/building/REAL250005035722 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035722 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035722/0 /scratch/stefan/7916117/working/building/REAL250005035722 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/285 `/scratch/stefan/7916117/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035722.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035722 none CCCCCC(C)CC(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 162, 162, 132, 116, 132, 44, 44, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 187, 187, 162, 162, 162, 162, 130, 132, 132, 132, 121, 121, 43, 9, 8, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 885 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035722 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035722 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035722/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035722 Building REAL250005035723 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035723' /scratch/stefan/7916117/working/building/REAL250005035723 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035723 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035723/0 /scratch/stefan/7916117/working/building/REAL250005035723 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/286 `/scratch/stefan/7916117/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1CCCC1) `REAL250005035723.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035723 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 16, 16, 16, 64, 88, 186, 186, 186, 186, 186, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 64, 64, 88, 88, 1, 1, 1, 1, 1, 1, 1, 1, 1] 186 rigid atoms, others: [32, 1, 34, 35, 33, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005035723 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 95, 95, 95, 24, 8, 1, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 186, 186, 186, 186, 95, 24, 24, 8, 8, 186, 186, 186, 186, 186, 186, 186, 186, 186] 186 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 727 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035723 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035723 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035723/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035723 Building REAL250005035724 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035724' /scratch/stefan/7916117/working/building/REAL250005035724 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035724 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035724/0 /scratch/stefan/7916117/working/building/REAL250005035724 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/287 `/scratch/stefan/7916117/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL250005035724.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035724 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 187, 99, 99, 99, 23, 8, 1, 1, 1, 1, 1, 1, 1, 187, 187, 187, 187, 187, 187, 187, 187, 99, 24, 24, 8, 8, 187] 187 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 441 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035724 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 69, 110, 187, 187, 187, 187, 187, 1, 1, 1, 2, 2, 2, 1, 1, 12, 69, 69, 110, 110, 1] 187 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 22, 23, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 601 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035724 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035724 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035724/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035724 Building REAL250005035725 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035725' /scratch/stefan/7916117/working/building/REAL250005035725 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035725 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035725/0 /scratch/stefan/7916117/working/building/REAL250005035725 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/288 `/scratch/stefan/7916117/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035725.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035725 none CCC(CC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 132, 60, 132, 186, 201, 201, 201, 201, 201, 60, 60, 19, 8, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 160, 132, 186, 186, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 19, 19, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 1138 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035725 none CCC(CC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 86, 95, 201, 201, 201, 201, 201, 10, 10, 10, 10, 10, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 86, 86, 95, 95] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 39, 37, 35, 36, 38, 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, 40, 41, 42, 43, 44]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035725 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035725 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035725/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035725 Building REAL250005035726 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035726' /scratch/stefan/7916117/working/building/REAL250005035726 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035726 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035726/0 /scratch/stefan/7916117/working/building/REAL250005035726 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/289 `/scratch/stefan/7916117/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035726.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035726 none CC1=CSC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 182, 87, 87, 87, 20, 8, 1, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 182, 87, 20, 20, 8, 8] 182 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 409 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: REAL250005035726 none CC1=CSC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 11, 11, 11, 59, 94, 182, 182, 182, 182, 182, 2, 2, 2, 1, 1, 11, 59, 59, 94, 94] 182 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26]) total number of confs: 554 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035726 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035726 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035726/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035726 Building REAL250005035727 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035727' /scratch/stefan/7916117/working/building/REAL250005035727 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035727 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035727/0 /scratch/stefan/7916117/working/building/REAL250005035727 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/290 `/scratch/stefan/7916117/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005035727.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035727 none CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 5, 1, 3, 11, 11, 11, 59, 82, 189, 189, 189, 189, 189, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 3, 11, 59, 59, 82, 82, 1, 1, 1, 1, 1] 201 rigid atoms, others: [19, 34, 3, 36, 37, 38, 15, 16, 17, 18, 35, 20] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 505 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035727 none CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 166, 180, 62, 62, 62, 20, 8, 1, 1, 1, 1, 1, 1, 1, 166, 189, 189, 166, 189, 189, 180, 180, 180, 180, 180, 180, 180, 166, 62, 20, 20, 8, 8, 189, 189, 166, 189, 189] 201 rigid atoms, others: [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, 33, 34, 35, 36, 37, 38]) total number of confs: 816 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035727 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035727 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035727/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035727 Building REAL250005035728 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035728' /scratch/stefan/7916117/working/building/REAL250005035728 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035728 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035728/0 /scratch/stefan/7916117/working/building/REAL250005035728 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/291 `/scratch/stefan/7916117/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2NC=CC2=CC=C1) `REAL250005035728.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035728 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2NC=CC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 60, 80, 171, 171, 171, 171, 171, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 60, 60, 80, 80, 1, 1, 1, 1, 1, 1] 171 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 472 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035728 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2NC=CC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 22, 8, 1, 1, 1, 1, 1, 1, 1, 84, 171, 171, 171, 171, 171, 171, 171, 171, 84, 22, 22, 8, 8, 171, 171, 171, 171, 171, 171] 171 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035728 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035728 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035728/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035728 Building REAL250005035729 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035729' /scratch/stefan/7916117/working/building/REAL250005035729 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035729 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035729/0 /scratch/stefan/7916117/working/building/REAL250005035729 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/292 `/scratch/stefan/7916117/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC(F)=CC=C1F)NCCC1=NC(=O)O[N-]1) `REAL250005035729.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035729 none O=C(CC1=CC(F)=CC=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 15, 1, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [34, 34, 34, 107, 201, 201, 201, 201, 201, 201, 201, 13, 7, 1, 1, 1, 1, 1, 1, 1, 107, 107, 201, 201, 201, 34, 13, 13, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 547 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035729 none O=C(CC1=CC(F)=CC=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 15, 1, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [36, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 116, 116, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 36, 116, 116, 116, 116] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035729 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035729 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035729/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035729 Building REAL250005035730 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035730' /scratch/stefan/7916117/working/building/REAL250005035730 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035730 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035730/0 /scratch/stefan/7916117/working/building/REAL250005035730 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/293 `/scratch/stefan/7916117/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005035730.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035730 none N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 148, 81, 81, 81, 22, 8, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 80, 22, 22, 8, 8] 148 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24]) 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: REAL250005035730 none N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 69, 86, 148, 148, 148, 148, 148, 1, 1, 1, 13, 69, 69, 86, 86] 148 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035730 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035730 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035730/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035730 Building REAL250005035731 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035731' /scratch/stefan/7916117/working/building/REAL250005035731 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035731 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035731/0 /scratch/stefan/7916117/working/building/REAL250005035731 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/294 `/scratch/stefan/7916117/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005035731.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035731 none CC1=CC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 184, 184, 102, 102, 102, 22, 8, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 184, 184, 184, 102, 22, 22, 8, 8] 184 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 433 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: REAL250005035731 none CC1=CC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 61, 93, 184, 184, 184, 184, 184, 1, 2, 2, 2, 1, 2, 2, 2, 11, 61, 61, 93, 93] 184 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 21] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 540 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035731 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035731 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035731/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035731 Building REAL250005035732 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035732' /scratch/stefan/7916117/working/building/REAL250005035732 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035732 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035732/0 /scratch/stefan/7916117/working/building/REAL250005035732 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/295 `/scratch/stefan/7916117/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C=CC=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035732.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035732 none O=C(CCN1C=CC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 178, 197, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 177, 177, 197, 197, 201, 201, 201, 201, 73, 20, 20, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035732 none O=C(CCN1C=CC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 15, 8, 1, 1, 1, 1, 1, 1, 55, 55, 127, 130, 201, 201, 201, 201, 201, 15, 15, 8, 8, 1, 1, 1, 1, 55, 127, 127, 130, 130] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035732 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035732 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035732/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035732 Building REAL250005035733 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035733' /scratch/stefan/7916117/working/building/REAL250005035733 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035733 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035733/0 /scratch/stefan/7916117/working/building/REAL250005035733 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/296 `/scratch/stefan/7916117/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CNN=C2C1) `REAL250005035733.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035733 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CNN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 8, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 72, 101, 165, 165, 165, 165, 165, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 72, 72, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1, 1] 165 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 522 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035733 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CNN=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 8, 8, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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] 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: [86, 86, 24, 8, 1, 1, 1, 1, 1, 1, 1, 85, 165, 165, 165, 165, 165, 165, 165, 165, 85, 24, 24, 8, 8, 165, 165, 165, 165, 165, 165, 165, 165, 165] 165 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 513 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035733 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035733 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035733/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035733 Building REAL250005035734 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035734' /scratch/stefan/7916117/working/building/REAL250005035734 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035734 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035734/0 /scratch/stefan/7916117/working/building/REAL250005035734 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/297 `/scratch/stefan/7916117/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(OC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035734.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035734 none CC(C)(OC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [145, 52, 145, 143, 201, 201, 201, 201, 201, 201, 52, 52, 8, 8, 1, 1, 1, 1, 1, 1, 1, 149, 145, 149, 149, 149, 145, 201, 201, 201, 201, 201, 52, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 625 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035734 none CC(C)(OC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [14, 4, 14, 1, 1, 1, 1, 1, 1, 1, 14, 47, 47, 47, 129, 129, 201, 201, 201, 201, 201, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 47, 129, 129, 129, 129] 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]) total number of confs: 623 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035734 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035734 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035734/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035734 Building REAL250005035735 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035735' /scratch/stefan/7916117/working/building/REAL250005035735 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035735 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035735/0 /scratch/stefan/7916117/working/building/REAL250005035735 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/298 `/scratch/stefan/7916117/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1) `REAL250005035735.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035735 none NC(=O)CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 177, 201, 105, 105, 105, 54, 54, 54, 19, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 201, 201, 177, 177, 105, 54, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035735 none NC(=O)CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [28, 6, 28, 1, 1, 1, 1, 1, 7, 7, 7, 31, 34, 105, 105, 105, 105, 105, 1, 1, 28, 28, 6, 6, 1, 7, 31, 31, 34, 34] 201 rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 24] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035735 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035735 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035735/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035735 Building REAL250005035736 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035736' /scratch/stefan/7916117/working/building/REAL250005035736 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035736 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035736/0 /scratch/stefan/7916117/working/building/REAL250005035736 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/299 `/scratch/stefan/7916117/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035736.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035736 none C#CCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 143, 47, 47, 97, 97, 47, 47, 47, 19, 8, 1, 1, 1, 1, 1, 1, 1, 97, 97, 201, 201, 201, 97, 97, 47, 19, 19, 8, 8, 97, 97] 201 rigid atoms, others: [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]) total number of confs: 785 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035736 none C#CCOC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 35, 97, 97, 97, 97, 97, 1, 1, 9, 9, 9, 1, 1, 5, 29, 29, 35, 35, 1, 1] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 19, 20, 24, 25, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035736 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035736 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035736/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035736 Building REAL250005035737 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035737' /scratch/stefan/7916117/working/building/REAL250005035737 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035737 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035737/0 /scratch/stefan/7916117/working/building/REAL250005035737 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/300 `/scratch/stefan/7916117/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NCCC1=NC(=O)O[N-]1)C(C)(C)C) `REAL250005035737.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035737 none CC(=CC(=O)NCCC1=NC(=O)O[N-]1)C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 76, 76, 76, 20, 8, 1, 1, 1, 1, 1, 1, 1, 132, 201, 201, 201, 132, 132, 132, 132, 75, 20, 20, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035737 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035737 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035737/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035737 Building REAL250005035738 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035738' /scratch/stefan/7916117/working/building/REAL250005035738 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035738 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035738/0 /scratch/stefan/7916117/working/building/REAL250005035738 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/301 `/scratch/stefan/7916117/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035738.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035738 none C=CCOCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 121, 105, 64, 81, 25, 25, 25, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 93, 94, 90, 90, 81, 81, 25, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 961 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035738 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035738 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035738/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035738 Building REAL250005035739 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035739' /scratch/stefan/7916117/working/building/REAL250005035739 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035739 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035739/0 /scratch/stefan/7916117/working/building/REAL250005035739 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/302 `/scratch/stefan/7916117/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC1C1CCCCC1) `REAL250005035739.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035739 none O=C(NCCC1=NC(=O)O[N-]1)C1CC1C1CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 66, 94, 201, 201, 201, 201, 201, 1, 1, 1, 1, 3, 3, 3, 3, 3, 13, 66, 66, 94, 94, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 201 rigid atoms, others: [1, 11, 12, 13, 14, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 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: REAL250005035739 none O=C(NCCC1=NC(=O)O[N-]1)C1CC1C1CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 201, 201, 201, 87, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035739 none O=C(NCCC1=NC(=O)O[N-]1)C1CC1C1CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 24, 24, 81, 103, 201, 201, 201, 201, 201, 3, 3, 1, 1, 1, 1, 1, 1, 1, 24, 81, 81, 103, 103, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 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]) total number of confs: 561 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035739 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035739 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035739/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035739 Building REAL250005035740 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035740' /scratch/stefan/7916117/working/building/REAL250005035740 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035740 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035740/0 /scratch/stefan/7916117/working/building/REAL250005035740 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/303 `/scratch/stefan/7916117/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035740.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035740 none CC(C)CC(=O)NCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 135, 135, 135, 129, 116, 47, 47, 47, 18, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 130, 130, 116, 116, 47, 18, 18, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 948 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035740 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035740 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035740/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035740 Building REAL250005035741 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035741' /scratch/stefan/7916117/working/building/REAL250005035741 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035741 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035741/0 /scratch/stefan/7916117/working/building/REAL250005035741 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/304 `/scratch/stefan/7916117/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CSC(F)(F)F)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035741.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035741 none CC(CSC(F)(F)F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 15, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [107, 38, 107, 141, 201, 201, 201, 201, 38, 38, 15, 7, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 141, 141, 38, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 753 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035741 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035741 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035741/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035741 Building REAL250005035742 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035742' /scratch/stefan/7916117/working/building/REAL250005035742 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035742 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035742/0 /scratch/stefan/7916117/working/building/REAL250005035742 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/305 `/scratch/stefan/7916117/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=CN=CC=C21) `REAL250005035742.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035742 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=CN=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [10, 1, 10, 10, 54, 89, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 54, 54, 89, 89, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 553 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035742 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=CN=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 24, 8, 1, 1, 1, 1, 1, 1, 1, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035742 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035742 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035742/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035742 Building REAL250005035743 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035743' /scratch/stefan/7916117/working/building/REAL250005035743 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035743 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035743/0 /scratch/stefan/7916117/working/building/REAL250005035743 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/306 `/scratch/stefan/7916117/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC(F)(F)F)NCCC1=NC(=O)O[N-]1) `REAL250005035743.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035743 none O=C(CCC(F)(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [70, 70, 70, 179, 163, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 179, 179, 201, 201, 69, 20, 19, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 1078 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035743 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035743 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035743/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035743 Building REAL250005035744 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035744' /scratch/stefan/7916117/working/building/REAL250005035744 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035744 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035744/0 /scratch/stefan/7916117/working/building/REAL250005035744 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/307 `/scratch/stefan/7916117/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCOCC2) `REAL250005035744.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035744 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCOCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 36, 50, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 1, 1, 7, 36, 36, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 117 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005035744 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCOCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 22, 8, 1, 1, 1, 1, 1, 1, 1, 72, 117, 117, 117, 117, 117, 117, 117, 71, 23, 23, 8, 8, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117] 117 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035744 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035744 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035744/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035744 Building REAL250005035745 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035745' /scratch/stefan/7916117/working/building/REAL250005035745 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005035745 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035745/0 /scratch/stefan/7916117/working/building/REAL250005035745 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/308 `/scratch/stefan/7916117/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035745.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035745 none C[N@@H+]1CCCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 53, 59, 53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 53, 17, 17, 8, 8] 59 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL250005035745 none C[N@@H+]1CCCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 22, 27, 59, 59, 59, 59, 59, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 27, 27] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035745 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035745/1 /scratch/stefan/7916117/working/building/REAL250005035745 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/309 `/scratch/stefan/7916117/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035745.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035745 none C[N@H+]1CCCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 73, 73, 63, 73, 63, 63, 17, 9, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 63, 17, 17, 9, 9] 73 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035745 none C[N@H+]1CCCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 25, 34, 73, 73, 73, 73, 73, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 25, 25, 34, 34] 73 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035745 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `2' /scratch/stefan/7916117/working/building/REAL250005035745/2 /scratch/stefan/7916117/working/building/REAL250005035745 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 2 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/310 `/scratch/stefan/7916117/working/3D/310' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035745.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005035745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035745/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035745 none CN1CCCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 126, 126, 89, 126, 89, 89, 25, 9, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 89, 25, 25, 9, 9] 126 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035745 none CN1CCCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 40, 61, 126, 126, 126, 126, 126, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 40, 40, 61, 61] 126 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27, 28, 29] set([32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 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/7916117/working/building/REAL250005035745 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035745 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035745/0.* 2: /scratch/stefan/7916117/working/building/REAL250005035745/2.* 1: /scratch/stefan/7916117/working/building/REAL250005035745/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035745 Building REAL250005035746 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035746' /scratch/stefan/7916117/working/building/REAL250005035746 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035746 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035746/0 /scratch/stefan/7916117/working/building/REAL250005035746 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/311 `/scratch/stefan/7916117/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=N1) `REAL250005035746.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035746 none CC(C)(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 86, 63, 63, 63, 24, 8, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 63, 25, 25, 8, 8, 86] 86 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL250005035746 none CC(C)(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 17, 29, 86, 86, 86, 86, 86, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 29, 29, 1] 86 rigid atoms, others: [1, 34, 4, 5, 6, 17, 18, 19] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035746 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035746 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035746/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035746 Building REAL250005035747 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035747' /scratch/stefan/7916117/working/building/REAL250005035747 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035747 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035747/0 /scratch/stefan/7916117/working/building/REAL250005035747 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/312 `/scratch/stefan/7916117/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCCCC1)NCCC1=NC(=O)O[N-]1) `REAL250005035747.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035747 none O=C(CC1CCCCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 160, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 160, 160, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 53, 19, 19, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 766 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035747 none O=C(CC1CCCCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 97, 101, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 97, 97, 101, 101] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035747 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035747 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035747/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035747 Building REAL250005035748 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035748' /scratch/stefan/7916117/working/building/REAL250005035748 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035748 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035748/0 /scratch/stefan/7916117/working/building/REAL250005035748 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/313 `/scratch/stefan/7916117/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC1=CC=CC=C1Cl)NCCC1=NC(=O)O[N-]1) `REAL250005035748.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035748 none O=C(CNC1=CC=CC=C1Cl)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 16, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [44, 44, 44, 152, 195, 201, 201, 195, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 152, 152, 195, 201, 201, 195, 201, 43, 8, 8, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 729 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035748 none O=C(CNC1=CC=CC=C1Cl)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 1, 16, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [65, 24, 4, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 121, 121, 201, 201, 201, 201, 201, 24, 24, 4, 1, 1, 1, 1, 66, 121, 121, 121, 121] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 589 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035748 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035748 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035748/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035748 Building REAL250005035749 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035749' /scratch/stefan/7916117/working/building/REAL250005035749 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035749 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035749/0 /scratch/stefan/7916117/working/building/REAL250005035749 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/314 `/scratch/stefan/7916117/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C([O-])C(F)=C1) `REAL250005035749.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035749 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C([O-])C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 12, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 24, 34, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 34, 34, 1, 1] 61 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035749 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=C([O-])C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 12, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 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: [43, 43, 24, 8, 1, 1, 1, 1, 1, 1, 1, 43, 58, 58, 58, 58, 58, 58, 58, 58, 43, 24, 24, 8, 8, 58, 58] 58 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035749 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035749 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035749/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035749 Building REAL250005035750 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035750' /scratch/stefan/7916117/working/building/REAL250005035750 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035750 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035750/0 /scratch/stefan/7916117/working/building/REAL250005035750 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/315 `/scratch/stefan/7916117/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CN(C)N=C1) `REAL250005035750.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035750 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 47, 47, 117, 119, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 13, 13, 13, 12, 47, 117, 117, 119, 119, 1, 2, 2, 2, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 603 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035750 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 45, 45, 16, 8, 1, 1, 1, 1, 1, 1, 1, 133, 201, 201, 201, 201, 201, 133, 133, 133, 133, 45, 16, 16, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035750 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035750 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035750/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035750 Building REAL250005035751 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035751' /scratch/stefan/7916117/working/building/REAL250005035751 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035751 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035751/0 /scratch/stefan/7916117/working/building/REAL250005035751 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/316 `/scratch/stefan/7916117/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CCCC(=O)NCCC2=NC(=O)O[N-]2)=CS1) `REAL250005035751.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035751 none CC1=NC(CCCC(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 139, 101, 98, 31, 31, 31, 13, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 136, 136, 131, 131, 98, 98, 31, 13, 13, 6, 6, 201] 201 rigid atoms, others: [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]) total number of confs: 873 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035751 none CC1=NC(CCCC(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 8, 19, 46, 46, 46, 108, 108, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 6, 6, 10, 10, 18, 18, 46, 108, 108, 108, 108, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 34, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035751 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035751 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035751/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035751 Building REAL250005035752 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035752' /scratch/stefan/7916117/working/building/REAL250005035752 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035752 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035752/0 /scratch/stefan/7916117/working/building/REAL250005035752 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/317 `/scratch/stefan/7916117/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(N2C=CC=C2)N=C1) `REAL250005035752.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035752 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(N2C=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 31, 54, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 5, 31, 31, 54, 54, 1, 1, 4, 4, 4, 4, 1] 105 rigid atoms, others: [1, 33, 11, 12, 13, 14, 15, 20, 21, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32]) 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: REAL250005035752 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(N2C=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 24, 8, 1, 1, 1, 1, 1, 1, 1, 55, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105, 55, 24, 24, 8, 8, 105, 105, 105, 105, 105, 105, 105] 105 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035752 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(N2C=CC=C2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [9, 3, 9, 9, 46, 69, 106, 106, 106, 106, 106, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 9, 46, 46, 69, 69, 3, 3, 1, 1, 1, 1, 3] 106 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 361 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035752 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035752 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035752/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035752 Building REAL250005035753 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035753' /scratch/stefan/7916117/working/building/REAL250005035753 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035753 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035753/0 /scratch/stefan/7916117/working/building/REAL250005035753 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/318 `/scratch/stefan/7916117/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035753.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035753 none CCCCCC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 141, 107, 95, 87, 39, 87, 87, 39, 39, 15, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 195, 153, 153, 107, 107, 107, 107, 87, 87, 87, 87, 87, 87, 39, 15, 15, 6, 6] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 994 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035753 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035753 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035753/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035753 Building REAL250005035754 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035754' /scratch/stefan/7916117/working/building/REAL250005035754 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035754 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035754/0 /scratch/stefan/7916117/working/building/REAL250005035754 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/319 `/scratch/stefan/7916117/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=COC=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035754.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035754 none O=C(CCC1=COC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 12, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [49, 49, 49, 133, 139, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 139, 139, 201, 201, 201, 49, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 668 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035754 none O=C(CCC1=COC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 12, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [35, 8, 4, 1, 1, 1, 1, 1, 1, 35, 35, 116, 121, 201, 201, 201, 201, 201, 8, 8, 4, 4, 1, 1, 1, 35, 118, 118, 121, 121] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 610 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035754 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035754 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035754/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035754 Building REAL250005035755 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035755' /scratch/stefan/7916117/working/building/REAL250005035755 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035755 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035755/0 /scratch/stefan/7916117/working/building/REAL250005035755 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/320 `/scratch/stefan/7916117/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035755.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035755 none CC(C)CC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 92, 62, 92, 92, 62, 62, 22, 8, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 62, 23, 23, 8, 8] 92 rigid atoms, others: [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, 36, 37]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035755 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035755 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035755/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035755 Building REAL250005035756 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035756' /scratch/stefan/7916117/working/building/REAL250005035756 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035756 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035756/0 /scratch/stefan/7916117/working/building/REAL250005035756 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/321 `/scratch/stefan/7916117/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1CCCOC1)NCCC1=NC(=O)O[N-]1) `REAL250005035756.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035756 none O=C(CCC1CCCOC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 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: [54, 54, 54, 156, 166, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 156, 156, 176, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 54, 17, 17, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 852 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035756 none O=C(CCC1CCCOC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 8, 5, 1, 1, 1, 1, 1, 1, 1, 35, 35, 116, 120, 201, 201, 201, 201, 201, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 116, 116, 120, 120] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 34, 36, 33, 35, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 593 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035756 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035756 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035756/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035756 Building REAL250005035757 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035757' /scratch/stefan/7916117/working/building/REAL250005035757 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035757 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035757/0 /scratch/stefan/7916117/working/building/REAL250005035757 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/322 `/scratch/stefan/7916117/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C1=O) `REAL250005035757.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035757 none CN1C(=O)NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 112, 112, 112, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 112, 23, 23, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 464 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035757 none CN1C(=O)NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 78, 114, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 13, 78, 78, 114, 114] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 625 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035757 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035757 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035757/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035757 Building REAL250005035758 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035758' /scratch/stefan/7916117/working/building/REAL250005035758 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035758 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035758/0 /scratch/stefan/7916117/working/building/REAL250005035758 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/323 `/scratch/stefan/7916117/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CN=C21) `REAL250005035758.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035758 none CN1N=CC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 47, 47, 47, 22, 8, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 106, 106, 106, 47, 22, 22, 8, 8, 106] 106 rigid atoms, others: [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]) 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: REAL250005035758 none CN1N=CC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 58, 106, 106, 106, 106, 106, 1, 1, 1, 2, 2, 2, 1, 1, 7, 33, 33, 58, 58, 1] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 24, 25, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 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/7916117/working/building/REAL250005035758 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035758 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035758/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035758 Building REAL250005035759 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035759' /scratch/stefan/7916117/working/building/REAL250005035759 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035759 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035759/0 /scratch/stefan/7916117/working/building/REAL250005035759 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/324 `/scratch/stefan/7916117/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOC1CCOCC1)NCCC1=NC(=O)O[N-]1) `REAL250005035759.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035759 none O=C(CCOC1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [58, 58, 58, 127, 127, 138, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201, 58, 19, 19, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035759 none O=C(CCOC1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 12, 10, 5, 1, 1, 1, 1, 1, 1, 1, 44, 44, 91, 96, 201, 201, 201, 201, 201, 12, 12, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 91, 91, 96, 96] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37]) total number of confs: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035759 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035759 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035759/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035759 Building REAL250005035760 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035760' /scratch/stefan/7916117/working/building/REAL250005035760 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035760 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035760/0 /scratch/stefan/7916117/working/building/REAL250005035760 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/325 `/scratch/stefan/7916117/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(C(=O)NCCC2=NC(=O)O[N-]2)C1(C)C) `REAL250005035760.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035760 none CC1(C)C(C(=O)NCCC2=NC(=O)O[N-]2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 65, 65, 65, 24, 8, 1, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 65, 24, 24, 8, 8, 100, 100, 100, 100, 100, 100] 100 rigid atoms, others: [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, 33, 34, 35]) 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: REAL250005035760 none CC1(C)C(C(=O)NCCC2=NC(=O)O[N-]2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 4, 4, 4, 24, 38, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 24, 24, 38, 38, 1, 1, 1, 2, 2, 2] 100 rigid atoms, others: [0, 1, 2, 3, 4, 32, 15, 16, 17, 18, 19, 20, 24, 30, 31] set([33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035760 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035760 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035760/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035760 Building REAL250005035761 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035761' /scratch/stefan/7916117/working/building/REAL250005035761 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035761 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035761/0 /scratch/stefan/7916117/working/building/REAL250005035761 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/326 `/scratch/stefan/7916117/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NC2=CC=CC=C21) `REAL250005035761.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035761 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 81, 81, 81, 23, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 81, 23, 23, 8, 8, 128, 128, 128, 128, 128] 128 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 337 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035761 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 44, 70, 128, 128, 128, 128, 128, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 44, 44, 70, 70, 1, 1, 1, 1, 1] 128 rigid atoms, others: [0, 1, 2, 3, 33, 32, 34, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035761 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035761 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035761/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035761 Building REAL250005035762 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035762' /scratch/stefan/7916117/working/building/REAL250005035762 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035762 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035762/0 /scratch/stefan/7916117/working/building/REAL250005035762 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/327 `/scratch/stefan/7916117/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(F)C=C1F) `REAL250005035762.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035762 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 103, 103, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 23, 23, 8, 8, 201] 201 rigid atoms, others: [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]) total number of confs: 458 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035762 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(F)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 13, 13, 13, 72, 114, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13, 72, 72, 114, 114, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 23, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 634 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035762 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035762 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035762/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035762 Building REAL250005035763 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035763' /scratch/stefan/7916117/working/building/REAL250005035763 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035763 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035763/0 /scratch/stefan/7916117/working/building/REAL250005035763 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/328 `/scratch/stefan/7916117/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC=NC=C1Cl) `REAL250005035763.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035763 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC=NC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 8, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 35, 62, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 1, 7, 35, 35, 62, 62, 1, 1] 147 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 404 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035763 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC=NC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 8, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 24, 8, 1, 1, 1, 1, 1, 1, 1, 94, 147, 147, 147, 147, 147, 147, 94, 24, 24, 8, 8, 147, 147] 147 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035763 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035763 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035763/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035763 Building REAL250005035764 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035764' /scratch/stefan/7916117/working/building/REAL250005035764 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035764 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035764/0 /scratch/stefan/7916117/working/building/REAL250005035764 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/329 `/scratch/stefan/7916117/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NN=CN1)NCCC1=NC(=O)O[N-]1) `REAL250005035764.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035764 none O=C(CCC1=NN=CN1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 5, 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: [81, 81, 81, 180, 195, 201, 201, 201, 201, 24, 8, 1, 1, 1, 1, 1, 1, 1, 181, 181, 195, 195, 201, 201, 81, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 778 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035764 none O=C(CCC1=NN=CN1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 5, 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, 14, 9, 1, 1, 1, 1, 1, 1, 43, 43, 99, 116, 201, 201, 201, 201, 201, 14, 14, 9, 9, 1, 1, 43, 100, 100, 116, 116] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 626 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035764 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035764/1 /scratch/stefan/7916117/working/building/REAL250005035764 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/330 `/scratch/stefan/7916117/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NNC=N1)NCCC1=NC(=O)O[N-]1) `REAL250005035764.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035764 none O=C(CCC1=NNC=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [48, 48, 48, 122, 139, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 122, 122, 139, 139, 201, 201, 48, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 713 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035764 none O=C(CCC1=NNC=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [50, 22, 9, 1, 1, 1, 1, 1, 1, 50, 50, 104, 108, 201, 201, 201, 201, 201, 22, 22, 9, 9, 1, 1, 50, 104, 104, 108, 108] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 610 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035764 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035764 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035764/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035764/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035764 Building REAL250005035765 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035765' /scratch/stefan/7916117/working/building/REAL250005035765 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035765 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035765/0 /scratch/stefan/7916117/working/building/REAL250005035765 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/331 `/scratch/stefan/7916117/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1CCOC1)NCCC1=NC(=O)O[N-]1) `REAL250005035765.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035765 none O=C(CCC1CCOC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 141, 158, 201, 201, 201, 201, 16, 8, 1, 1, 1, 1, 1, 1, 1, 141, 141, 178, 178, 201, 201, 201, 201, 201, 201, 201, 48, 16, 16, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 924 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035765 none O=C(CCC1CCOC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 9, 5, 1, 1, 1, 1, 1, 1, 41, 41, 114, 114, 201, 201, 201, 201, 201, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 41, 115, 115, 115, 115] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31]) total number of confs: 583 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035765 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035765 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035765/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035765 Building REAL250005035766 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035766' /scratch/stefan/7916117/working/building/REAL250005035766 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035766 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035766/0 /scratch/stefan/7916117/working/building/REAL250005035766 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/332 `/scratch/stefan/7916117/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CSC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035766.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035766 none N#CC1=CSC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 180, 180, 85, 85, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 180, 180, 84, 24, 24, 8, 8, 180] 180 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 404 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035766 none N#CC1=CSC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 66, 99, 180, 180, 180, 180, 180, 1, 1, 13, 66, 66, 99, 99, 1] 180 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035766 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035766 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035766/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035766 Building REAL250005035767 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035767' /scratch/stefan/7916117/working/building/REAL250005035767 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035767 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035767/0 /scratch/stefan/7916117/working/building/REAL250005035767 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/333 `/scratch/stefan/7916117/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NN(C)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035767.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035767 none CC(C)C1=NN(C)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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, 5, 5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 165, 201, 165, 165, 165, 165, 75, 75, 75, 23, 8, 1, 1, 1, 1, 1, 1, 1, 165, 201, 201, 201, 201, 201, 201, 201, 165, 165, 165, 75, 24, 23, 8, 8, 165] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 602 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035767 none CC(C)C1=NN(C)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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, 5, 5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 38, 48, 165, 165, 165, 165, 165, 1, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 8, 38, 38, 48, 48, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 35] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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/7916117/working/building/REAL250005035767 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035767 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035767/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035767 Building REAL250005035768 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035768' /scratch/stefan/7916117/working/building/REAL250005035768 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035768 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035768/0 /scratch/stefan/7916117/working/building/REAL250005035768 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/334 `/scratch/stefan/7916117/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NN=C(CCC(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005035768.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035768 none CC(C)C1=NN=C(CCC(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 159, 201, 159, 159, 159, 118, 110, 31, 31, 31, 15, 7, 1, 1, 1, 1, 1, 1, 1, 159, 201, 201, 201, 201, 201, 201, 201, 118, 118, 110, 110, 31, 15, 15, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 802 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035768 none CC(C)C1=NN=C(CCC(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 1, 1, 1, 1, 1, 7, 13, 35, 36, 36, 59, 69, 159, 159, 159, 159, 159, 1, 12, 12, 12, 12, 12, 12, 12, 7, 7, 14, 13, 36, 59, 59, 69, 69] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 20] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035768 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035768 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035768/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035768 Building REAL250005035769 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035769' /scratch/stefan/7916117/working/building/REAL250005035769 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035769 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035769/0 /scratch/stefan/7916117/working/building/REAL250005035769 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/335 `/scratch/stefan/7916117/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CSCCS1) `REAL250005035769.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035769 none O=C(NCCC1=NC(=O)O[N-]1)C1CSCCS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 14, 5, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 76, 109, 181, 181, 181, 181, 181, 1, 1, 1, 1, 1, 1, 13, 76, 76, 109, 109, 1, 1, 1, 1, 1, 1, 1] 181 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 565 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: REAL250005035769 none O=C(NCCC1=NC(=O)O[N-]1)C1CSCCS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 14, 5, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 96, 181, 181, 181, 181, 181, 96, 25, 24, 8, 8, 181, 181, 181, 181, 181, 181, 181] 181 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 562 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035769 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035769 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035769/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035769 Building REAL250005035770 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035770' /scratch/stefan/7916117/working/building/REAL250005035770 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035770 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035770/0 /scratch/stefan/7916117/working/building/REAL250005035770 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/336 `/scratch/stefan/7916117/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1) `REAL250005035770.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035770 none COC(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 126, 201, 126, 126, 55, 55, 55, 19, 8, 1, 1, 1, 1, 1, 1, 1, 126, 126, 126, 201, 201, 201, 126, 55, 19, 19, 8, 8, 126, 126] 201 rigid atoms, others: [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]) 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: REAL250005035770 none COC(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [11, 11, 1, 11, 1, 1, 1, 1, 5, 5, 5, 28, 32, 126, 126, 126, 126, 126, 1, 1, 1, 11, 11, 11, 1, 5, 28, 28, 32, 32, 1, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 18, 19, 20, 24, 30, 31] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035770 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035770 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035770/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035770 Building REAL250005035771 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035771' /scratch/stefan/7916117/working/building/REAL250005035771 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035771 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035771/0 /scratch/stefan/7916117/working/building/REAL250005035771 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/337 `/scratch/stefan/7916117/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C) `REAL250005035771.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035771 none CC(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 162, 94, 94, 94, 24, 8, 1, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 162, 162, 162, 162, 162, 162, 93, 24, 24, 8, 8, 162, 162, 162] 162 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 391 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035771 none CC(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 13, 13, 13, 57, 77, 162, 162, 162, 162, 162, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 13, 57, 57, 77, 77, 2, 2, 2] 162 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 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 /scratch/stefan/7916117/working/building/REAL250005035771 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035771 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035771/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035771 Building REAL250005035772 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035772' /scratch/stefan/7916117/working/building/REAL250005035772 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035772 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035772/0 /scratch/stefan/7916117/working/building/REAL250005035772 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/338 `/scratch/stefan/7916117/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC=C2)CC1) `REAL250005035772.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035772 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 151, 151, 151, 151, 151, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 6, 27, 27, 39, 39, 6, 6, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 33, 11, 12, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 325 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: REAL250005035772 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 78, 23, 8, 1, 1, 1, 1, 1, 1, 1, 78, 151, 201, 201, 201, 201, 201, 201, 151, 151, 78, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201, 151, 151, 151, 151] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 764 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: REAL250005035772 none O=C(NCCC1=NC(=O)O[N-]1)C1(CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 91, 105, 201, 201, 201, 201, 201, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 91, 91, 105, 105, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36]) total number of confs: 580 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035772 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035772 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035772/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035772 Building REAL250005035773 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035773' /scratch/stefan/7916117/working/building/REAL250005035773 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035773 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035773/0 /scratch/stefan/7916117/working/building/REAL250005035773 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/339 `/scratch/stefan/7916117/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035773.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035773 none CCCC1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', '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, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 167, 106, 106, 106, 106, 62, 62, 62, 19, 8, 1, 1, 1, 1, 1, 1, 1, 106, 201, 201, 201, 201, 201, 167, 167, 106, 62, 19, 19, 8, 8, 106] 201 rigid atoms, others: [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]) total number of confs: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035773 none CCCC1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', '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, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [13, 9, 1, 1, 1, 1, 1, 1, 7, 7, 7, 35, 40, 106, 106, 106, 106, 106, 1, 15, 15, 15, 15, 15, 9, 9, 1, 7, 35, 35, 40, 40, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 18, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035773 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035773 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035773/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035773 Building REAL250005035774 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035774' /scratch/stefan/7916117/working/building/REAL250005035774 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035774 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035774/0 /scratch/stefan/7916117/working/building/REAL250005035774 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/340 `/scratch/stefan/7916117/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035774.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035774 none CC(C)CC1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [178, 178, 201, 89, 89, 89, 89, 59, 59, 59, 19, 8, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 201, 201, 178, 178, 89, 59, 19, 19, 8, 8, 89] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 952 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035774 none CC(C)CC1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 39, 89, 89, 89, 89, 89, 1, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 7, 33, 33, 39, 39, 1] 201 rigid atoms, others: [35, 3, 4, 5, 6, 7, 8, 19, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035774 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035774 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035774/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035774 Building REAL250005035775 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035775' /scratch/stefan/7916117/working/building/REAL250005035775 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035775 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035775/0 /scratch/stefan/7916117/working/building/REAL250005035775 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/341 `/scratch/stefan/7916117/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035775.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035775 none CC(C)(C)C1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 118, 198, 198, 118, 118, 118, 64, 64, 64, 24, 8, 1, 1, 1, 1, 1, 1, 1, 118, 198, 198, 198, 198, 198, 198, 198, 198, 198, 118, 64, 24, 24, 8, 8, 118] 198 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035775 none CC(C)(C)C1=NNC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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, 5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 10, 10, 11, 55, 72, 118, 118, 118, 118, 118, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 11, 55, 55, 72, 72, 1] 198 rigid atoms, others: [1, 35, 4, 5, 6, 7, 8, 19, 29] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035775 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035775 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035775/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035775 Building REAL250005035776 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035776' /scratch/stefan/7916117/working/building/REAL250005035776 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035776 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035776/0 /scratch/stefan/7916117/working/building/REAL250005035776 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/342 `/scratch/stefan/7916117/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CS(C)(=O)=O)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035776.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035776 none CC(CS(C)(=O)=O)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 11, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 7, 8, 8, 8, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 8, 8, 8, 6, 6, 6, 6, 6] 8 rigid atoms, others: [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]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035776 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035776 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035776/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035776 Building REAL250005035777 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035777' /scratch/stefan/7916117/working/building/REAL250005035777 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035777 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035777/0 /scratch/stefan/7916117/working/building/REAL250005035777 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/343 `/scratch/stefan/7916117/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CSC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035777.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035777 none COC1=CSC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 154, 154, 154, 154, 82, 82, 82, 21, 8, 1, 1, 1, 1, 1, 1, 1, 154, 201, 201, 201, 154, 82, 21, 21, 8, 8, 154] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 462 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035777 none COC1=CSC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 52, 65, 154, 154, 154, 154, 154, 1, 2, 2, 2, 1, 13, 52, 52, 65, 65, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 21, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035777 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035777 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035777/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035777 Building REAL250005035778 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035778' /scratch/stefan/7916117/working/building/REAL250005035778 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035778 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035778/0 /scratch/stefan/7916117/working/building/REAL250005035778 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/344 `/scratch/stefan/7916117/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035778.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035778 none CC(C)CCCCCC(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 163, 169, 175, 130, 128, 45, 45, 45, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 162, 162, 128, 128, 45, 17, 17, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035778 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035778 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035778/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035778 Building REAL250005035779 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035779' /scratch/stefan/7916117/working/building/REAL250005035779 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035779 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035779/0 /scratch/stefan/7916117/working/building/REAL250005035779 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/345 `/scratch/stefan/7916117/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CCC(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005035779.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035779 none CC1=CC=C(CCC(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 162, 131, 39, 39, 39, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 162, 162, 131, 131, 39, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 775 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035779 none CC1=CC=C(CCC(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [1, 1, 1, 1, 1, 1, 7, 15, 62, 62, 62, 134, 136, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 7, 7, 15, 15, 62, 136, 136, 136, 136] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 666 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035779 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035779 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035779/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035779 Building REAL250005035780 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035780' /scratch/stefan/7916117/working/building/REAL250005035780 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035780 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035780/0 /scratch/stefan/7916117/working/building/REAL250005035780 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/346 `/scratch/stefan/7916117/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CCCC(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005035780.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035780 none CC1=CC=C(CCCC(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 130, 93, 87, 27, 27, 27, 11, 6, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 127, 128, 125, 125, 87, 87, 27, 11, 11, 6, 6] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 895 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035780 none CC1=CC=C(CCCC(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 6, 6, 12, 40, 40, 40, 104, 104, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 6, 6, 6, 6, 12, 12, 40, 104, 104, 104, 104] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035780 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035780 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035780/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035780 Building REAL250005035781 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035781' /scratch/stefan/7916117/working/building/REAL250005035781 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035781 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035781/0 /scratch/stefan/7916117/working/building/REAL250005035781 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/347 `/scratch/stefan/7916117/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005035781.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035781 none COC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 135, 135, 135, 81, 81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 135, 81, 24, 24, 8, 8] 135 rigid atoms, others: [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]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035781 none COC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 47, 66, 135, 135, 135, 135, 135, 1, 2, 2, 2, 1, 1, 1, 12, 47, 47, 66, 66] 135 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035781 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035781 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035781/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035781 Building REAL250005035782 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035782' /scratch/stefan/7916117/working/building/REAL250005035782 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035782 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035782/0 /scratch/stefan/7916117/working/building/REAL250005035782 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/348 `/scratch/stefan/7916117/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1CCOC1)NCCC1=NC(=O)O[N-]1) `REAL250005035782.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035782 none O=C(COC1CCOC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 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: [43, 43, 43, 144, 186, 201, 201, 201, 201, 18, 8, 1, 1, 1, 1, 1, 1, 1, 144, 144, 201, 201, 201, 201, 201, 201, 201, 43, 18, 18, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035782 none O=C(COC1CCOC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 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: [56, 20, 5, 1, 1, 1, 1, 1, 1, 56, 56, 128, 132, 201, 201, 201, 201, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1, 56, 128, 128, 132, 132] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31]) total number of confs: 629 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035782 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035782 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035782/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035782 Building REAL250005035783 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035783' /scratch/stefan/7916117/working/building/REAL250005035783 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035783 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035783/0 /scratch/stefan/7916117/working/building/REAL250005035783 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/349 `/scratch/stefan/7916117/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCCC2) `REAL250005035783.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035783 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 65, 96, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 1, 11, 65, 65, 96, 96, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 178 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 528 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: REAL250005035783 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 96, 178, 178, 178, 178, 178, 178, 96, 25, 25, 8, 8, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178, 178] 178 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 551 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035783 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035783 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035783/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035783 Building REAL250005035784 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035784' /scratch/stefan/7916117/working/building/REAL250005035784 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035784 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035784/0 /scratch/stefan/7916117/working/building/REAL250005035784 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/350 `/scratch/stefan/7916117/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(SC1=CC=CC=N1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035784.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035784 none CC(SC1=CC=CC=N1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [124, 41, 130, 184, 201, 201, 201, 201, 201, 41, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 130, 124, 130, 130, 201, 201, 201, 201, 40, 8, 8, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035784 none CC(SC1=CC=CC=N1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 9, 1, 1, 1, 1, 1, 1, 1, 25, 68, 68, 68, 133, 133, 201, 201, 201, 201, 201, 25, 25, 25, 25, 1, 1, 1, 1, 68, 133, 133, 133, 133] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32]) total number of confs: 640 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035784 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035784 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035784/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035784 Building REAL250005035785 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035785' /scratch/stefan/7916117/working/building/REAL250005035785 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035785 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035785/0 /scratch/stefan/7916117/working/building/REAL250005035785 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/351 `/scratch/stefan/7916117/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1=CC=C(O)C=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035785.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035785 none O=C(CCCC1=CC=C(O)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [32, 32, 32, 130, 144, 201, 201, 201, 201, 201, 201, 201, 13, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 186, 186, 201, 201, 201, 201, 402, 201, 201, 32, 13, 13, 8, 8] 402 rigid atoms, others: [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]) total number of confs: 1549 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035785 none O=C(CCCC1=CC=C(O)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 108, 108, 201, 201, 201, 201, 201, 5, 5, 3, 3, 1, 1, 1, 1, 2, 1, 1, 22, 108, 108, 108, 108] 402 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 30, 31] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 32, 33, 34, 35, 36]) total number of confs: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035785 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035785 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035785/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035785 Building REAL250005035786 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035786' /scratch/stefan/7916117/working/building/REAL250005035786 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035786 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035786/0 /scratch/stefan/7916117/working/building/REAL250005035786 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/352 `/scratch/stefan/7916117/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CC)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035786.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035786 none CCC(CC)(CC)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [161, 131, 51, 131, 129, 131, 163, 51, 51, 23, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 167, 167, 167, 167, 167, 51, 24, 23, 8, 8] 167 rigid atoms, others: [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, 36, 37]) total number of confs: 1477 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035786 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035786 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035786/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035786 Building REAL250005035787 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035787' /scratch/stefan/7916117/working/building/REAL250005035787 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035787 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035787/0 /scratch/stefan/7916117/working/building/REAL250005035787 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/353 `/scratch/stefan/7916117/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1) `REAL250005035787.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035787 none COCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 191, 145, 145, 58, 58, 58, 17, 8, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 201, 201, 201, 191, 191, 145, 145, 58, 17, 17, 8, 8, 145, 145, 145, 145, 145, 145] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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: REAL250005035787 none COCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 4, 1, 1, 1, 5, 5, 5, 29, 37, 145, 145, 145, 145, 145, 1, 1, 1, 17, 17, 17, 6, 6, 4, 4, 5, 29, 29, 37, 37, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 16, 17, 18, 35, 36, 31] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035787 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035787 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035787/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035787 Building REAL250005035788 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035788' /scratch/stefan/7916117/working/building/REAL250005035788 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035788 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035788/0 /scratch/stefan/7916117/working/building/REAL250005035788 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/354 `/scratch/stefan/7916117/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035788.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035788 none CCC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 191, 123, 191, 50, 123, 123, 50, 50, 50, 17, 8, 1, 1, 1, 1, 1, 1, 1, 123, 123, 201, 201, 201, 201, 201, 123, 123, 50, 17, 17, 8, 8, 123, 123] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 827 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035788 none CCC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [25, 6, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 29, 33, 123, 123, 123, 123, 123, 1, 1, 25, 25, 25, 25, 25, 1, 1, 5, 29, 29, 33, 33, 1, 1] 201 rigid atoms, others: [33, 2, 4, 5, 6, 7, 8, 34, 19, 20, 26, 27] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035788 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035788 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035788/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035788 Building REAL250005035789 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035789' /scratch/stefan/7916117/working/building/REAL250005035789 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035789 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035789/0 /scratch/stefan/7916117/working/building/REAL250005035789 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/355 `/scratch/stefan/7916117/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C#N)(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035789.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035789 none CC1CC(C#N)(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 96, 201, 201, 96, 96, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 96, 20, 20, 8, 8, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 617 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: REAL250005035789 none CC1CC(C#N)(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7, 46, 73, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 7, 46, 46, 73, 73, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 21, 22, 23, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 502 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035789 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035789 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035789/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035789 Building REAL250005035790 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035790' /scratch/stefan/7916117/working/building/REAL250005035790 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035790 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035790/0 /scratch/stefan/7916117/working/building/REAL250005035790 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/356 `/scratch/stefan/7916117/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2CC2)N1) `REAL250005035790.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035790 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2CC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 33, 41, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 13, 13, 1, 8, 33, 33, 41, 41, 1, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 24, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035790 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2CC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 19, 8, 1, 1, 1, 1, 1, 1, 1, 58, 104, 104, 104, 104, 201, 201, 104, 58, 19, 19, 8, 8, 104, 201, 201, 201, 201, 201, 104] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035790 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(C2CC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 13, 54, 54, 139, 150, 201, 201, 201, 201, 201, 13, 13, 13, 1, 1, 1, 1, 13, 54, 139, 139, 150, 150, 13, 1, 1, 1, 1, 1, 13] 201 rigid atoms, others: [14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 30]) total number of confs: 627 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035790 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035790 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035790/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035790 Building REAL250005035791 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035791' /scratch/stefan/7916117/working/building/REAL250005035791 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035791 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035791/0 /scratch/stefan/7916117/working/building/REAL250005035791 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/357 `/scratch/stefan/7916117/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035791.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035791 none CCC(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 149, 156, 102, 149, 149, 68, 68, 68, 21, 8, 1, 1, 1, 1, 1, 1, 1, 149, 149, 201, 201, 201, 201, 201, 156, 156, 156, 156, 149, 149, 67, 21, 21, 8, 8, 149, 149] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 891 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035791 none CCC(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)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', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 5, 5, 5, 29, 53, 149, 149, 149, 149, 149, 1, 1, 9, 9, 9, 9, 9, 6, 6, 6, 6, 1, 1, 5, 29, 29, 53, 53, 1, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 19, 20, 38, 37, 30, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035791 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035791 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035791/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035791 Building REAL250005035792 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035792' /scratch/stefan/7916117/working/building/REAL250005035792 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035792 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035792/0 /scratch/stefan/7916117/working/building/REAL250005035792 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/358 `/scratch/stefan/7916117/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=C1F) `REAL250005035792.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035792 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [12, 1, 12, 13, 72, 96, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 13, 72, 72, 96, 96, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005035792 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 99, 201, 201, 201, 201, 201, 201, 201, 99, 24, 24, 8, 8, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035792 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035792 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035792/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035792 Building REAL250005035793 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035793' /scratch/stefan/7916117/working/building/REAL250005035793 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035793 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035793/0 /scratch/stefan/7916117/working/building/REAL250005035793 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/359 `/scratch/stefan/7916117/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005035793.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035793 none CC(C)(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 119, 201, 201, 119, 119, 119, 68, 68, 68, 24, 8, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 68, 24, 24, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 801 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035793 none CC(C)(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 1, 12, 12, 13, 49, 64, 119, 119, 119, 119, 119, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 13, 49, 49, 64, 64] 201 rigid atoms, others: [1, 4, 5, 6, 7, 8, 19, 29, 30] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035793 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035793 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035793/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035793 Building REAL250005035794 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035794' /scratch/stefan/7916117/working/building/REAL250005035794 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035794 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035794/0 /scratch/stefan/7916117/working/building/REAL250005035794 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/360 `/scratch/stefan/7916117/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(F)=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL250005035794.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035794 none N#CC1=CC(F)=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 108, 108, 77, 77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 76, 24, 24, 8, 8, 108] 108 rigid atoms, others: [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]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035794 none N#CC1=CC(F)=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 49, 65, 108, 108, 108, 108, 108, 1, 1, 1, 1, 10, 49, 49, 65, 65, 1] 108 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035794 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035794 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035794/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035794 Building REAL250005035795 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035795' /scratch/stefan/7916117/working/building/REAL250005035795 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035795 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035795/0 /scratch/stefan/7916117/working/building/REAL250005035795 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/361 `/scratch/stefan/7916117/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(F)=C1CCCC1) `REAL250005035795.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035795 none O=C(NCCC1=NC(=O)O[N-]1)C(F)=C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 60, 94, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 10, 60, 60, 94, 94, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 564 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035795 none O=C(NCCC1=NC(=O)O[N-]1)C(F)=C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 24, 8, 1, 1, 1, 1, 1, 1, 1, 113, 201, 201, 201, 201, 201, 201, 113, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035795 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035795 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035795/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035795 Building REAL250005035796 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035796' /scratch/stefan/7916117/working/building/REAL250005035796 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035796 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035796/0 /scratch/stefan/7916117/working/building/REAL250005035796 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/362 `/scratch/stefan/7916117/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(F)C=C1F)NCCC1=NC(=O)O[N-]1) `REAL250005035796.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035796 none O=C(CC1=CC=C(F)C=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [36, 36, 36, 121, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 36, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035796 none O=C(CC1=CC=C(F)C=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 113, 115, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 33, 113, 113, 115, 115] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 582 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035796 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035796 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035796/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035796 Building REAL250005035797 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035797' /scratch/stefan/7916117/working/building/REAL250005035797 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035797 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035797/0 /scratch/stefan/7916117/working/building/REAL250005035797 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/363 `/scratch/stefan/7916117/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(F)C(F)=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035797.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035797 none O=C(CC1=CC=C(F)C(F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [50, 50, 50, 115, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 115, 115, 201, 201, 201, 50, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 622 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035797 none O=C(CC1=CC=C(F)C(F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 75, 81, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 17, 75, 75, 81, 81] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035797 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035797 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035797/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035797 Building REAL250005035798 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035798' /scratch/stefan/7916117/working/building/REAL250005035798 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035798 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035798/0 /scratch/stefan/7916117/working/building/REAL250005035798 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/364 `/scratch/stefan/7916117/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=C(F)C=CC=C1F)NCCC1=NC(=O)O[N-]1) `REAL250005035798.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035798 none O=C(CC1=C(F)C=CC=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 15, 1, 1, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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, 48, 47, 165, 201, 201, 201, 183, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 201, 201, 201, 47, 20, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 801 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035798 none O=C(CC1=C(F)C=CC=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 15, 1, 1, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 89, 95, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 19, 89, 89, 95, 95] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 521 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035798 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035798 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035798/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035798 Building REAL250005035799 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035799' /scratch/stefan/7916117/working/building/REAL250005035799 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035799 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035799/0 /scratch/stefan/7916117/working/building/REAL250005035799 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/365 `/scratch/stefan/7916117/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC1CC1=CC=CC=C1) `REAL250005035799.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035799 none O=C(NCCC1=NC(=O)O[N-]1)C1CC1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 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: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 52, 53, 138, 138, 138, 138, 138, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 11, 52, 52, 53, 53, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7] 201 rigid atoms, others: [1, 11, 12, 13, 14, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035799 none O=C(NCCC1=NC(=O)O[N-]1)C1CC1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 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: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 1, 1, 1, 1, 1, 1, 1, 44, 138, 138, 138, 192, 201, 201, 201, 201, 201, 44, 17, 17, 7, 7, 137, 138, 138, 138, 192, 192, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 711 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035799 none O=C(NCCC1=NC(=O)O[N-]1)C1CC1CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 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: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 7, 45, 45, 126, 127, 201, 201, 201, 201, 201, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 45, 126, 126, 127, 127, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1] 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]) total number of confs: 611 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035799 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035799 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035799/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035799 Building REAL250005035800 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035800' /scratch/stefan/7916117/working/building/REAL250005035800 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035800 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035800/0 /scratch/stefan/7916117/working/building/REAL250005035800 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/366 `/scratch/stefan/7916117/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CC(F)=C1F)NCCC1=NC(=O)O[N-]1) `REAL250005035800.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035800 none O=C(CC1=CC=CC(F)=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 15, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [41, 41, 41, 133, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 201, 201, 201, 41, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 592 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035800 none O=C(CC1=CC=CC(F)=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 15, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [37, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 114, 114, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 37, 114, 114, 114, 114] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035800 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035800 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035800/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035800 Building REAL250005035801 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035801' /scratch/stefan/7916117/working/building/REAL250005035801 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035801 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035801/0 /scratch/stefan/7916117/working/building/REAL250005035801 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/367 `/scratch/stefan/7916117/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C)OCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035801.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035801 none CC(C)CC(C)OCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 201, 166, 135, 46, 46, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 145, 145, 45, 9, 8, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 779 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035801 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035801 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035801/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035801 Building REAL250005035802 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035802' /scratch/stefan/7916117/working/building/REAL250005035802 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035802 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035802/0 /scratch/stefan/7916117/working/building/REAL250005035802 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/368 `/scratch/stefan/7916117/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCCO1)NCCC1=NC(=O)O[N-]1) `REAL250005035802.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035802 none O=C(CC1CCCCO1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 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: [63, 63, 63, 176, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 176, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 63, 19, 19, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035802 none O=C(CC1CCCCO1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 7, 1, 1, 1, 1, 1, 1, 1, 28, 28, 100, 106, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 100, 100, 106, 106] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035802 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035802 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035802/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035802 Building REAL250005035803 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035803' /scratch/stefan/7916117/working/building/REAL250005035803 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035803 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035803/0 /scratch/stefan/7916117/working/building/REAL250005035803 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/369 `/scratch/stefan/7916117/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)CCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035803.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035803 none CCN(CC)C(=O)CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [155, 93, 93, 93, 159, 91, 93, 91, 47, 47, 47, 17, 8, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 159, 159, 159, 159, 159, 91, 91, 91, 91, 47, 17, 17, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035803 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035803 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035803/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035803 Building REAL250005035804 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035804' /scratch/stefan/7916117/working/building/REAL250005035804 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035804 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035804/0 /scratch/stefan/7916117/working/building/REAL250005035804 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/370 `/scratch/stefan/7916117/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F) `REAL250005035804.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035804 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 164, 164, 164, 72, 72, 72, 21, 8, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 201, 201, 201, 164, 72, 21, 21, 8, 8, 164, 164] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 447 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035804 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 29, 53, 164, 164, 164, 164, 164, 1, 1, 1, 1, 4, 4, 4, 1, 5, 29, 29, 53, 53, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 23, 29, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035804 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035804 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035804/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035804 Building REAL250005035805 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035805' /scratch/stefan/7916117/working/building/REAL250005035805 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035805 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035805/0 /scratch/stefan/7916117/working/building/REAL250005035805 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/371 `/scratch/stefan/7916117/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035805.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035805 none CC1=CC(Cl)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 151, 151, 57, 57, 57, 20, 8, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 151, 57, 20, 20, 8, 8, 151] 151 rigid atoms, others: [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]) total number of confs: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035805 none CC1=CC(Cl)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 59, 151, 151, 151, 151, 151, 1, 2, 2, 2, 1, 1, 7, 39, 39, 59, 59, 1] 151 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 22, 23, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035805 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035805 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035805/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035805 Building REAL250005035806 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035806' /scratch/stefan/7916117/working/building/REAL250005035806 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035806 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035806/0 /scratch/stefan/7916117/working/building/REAL250005035806 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/372 `/scratch/stefan/7916117/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2CCCC2)C=C1) `REAL250005035806.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035806 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 42, 113, 113, 113, 113, 113, 1, 1, 1, 1, 10, 10, 10, 10, 1, 1, 7, 30, 30, 42, 42, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1] 201 rigid atoms, others: [1, 35, 36, 11, 12, 13, 14, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035806 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 1, 1, 1, 1, 1, 1, 1, 73, 113, 113, 113, 201, 201, 201, 201, 113, 113, 72, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 113] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035806 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 35, 35, 97, 122, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 1, 1, 1, 10, 10, 35, 97, 97, 122, 122, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 35, 36]) total number of confs: 610 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035806 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035806 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035806/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035806 Building REAL250005035807 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035807' /scratch/stefan/7916117/working/building/REAL250005035807 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035807 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035807/0 /scratch/stefan/7916117/working/building/REAL250005035807 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/373 `/scratch/stefan/7916117/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1) `REAL250005035807.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035807 none CC(C)CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 54, 54, 54, 23, 8, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 54, 23, 23, 8, 8, 93, 93, 93, 93, 93, 93, 93, 93] 93 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 324 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: REAL250005035807 none CC(C)CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 1, 1, 1, 4, 4, 4, 20, 35, 93, 93, 93, 93, 93, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1] 93 rigid atoms, others: [35, 34, 3, 4, 5, 38, 39, 40, 41, 16, 17, 18, 19, 36, 37] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 251 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035807 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035807 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035807/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035807 Building REAL250005035808 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035808' /scratch/stefan/7916117/working/building/REAL250005035808 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035808 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035808/0 /scratch/stefan/7916117/working/building/REAL250005035808 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/374 `/scratch/stefan/7916117/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(CC)=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035808.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035808 none CCC1=NOC(CC)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [124, 75, 75, 75, 75, 75, 75, 119, 48, 22, 22, 22, 11, 7, 1, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 119, 119, 119, 119, 119, 48, 48, 22, 11, 11, 7, 7] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 808 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035808 none CCC1=NOC(CC)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 6, 1, 1, 2, 9, 9, 9, 37, 37, 75, 75, 75, 75, 75, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 2, 2, 9, 37, 37, 37, 37] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 8, 9] set([0, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035808 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035808 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035808/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035808 Building REAL250005035809 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035809' /scratch/stefan/7916117/working/building/REAL250005035809 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035809 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035809/0 /scratch/stefan/7916117/working/building/REAL250005035809 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/375 `/scratch/stefan/7916117/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CC(=O)NCCC2=NC(=O)O[N-]2)=C(C)S1) `REAL250005035809.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035809 none CC1=NC(CC(=O)NCCC2=NC(=O)O[N-]2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 152, 36, 36, 36, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 152, 152, 36, 15, 15, 7, 7, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL250005035809 none CC1=NC(CC(=O)NCCC2=NC(=O)O[N-]2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 4, 30, 30, 31, 108, 110, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 4, 4, 30, 108, 108, 110, 110, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 16, 17, 18] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035809 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035809 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035809/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035809 Building REAL250005035810 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035810' /scratch/stefan/7916117/working/building/REAL250005035810 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035810 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035810/0 /scratch/stefan/7916117/working/building/REAL250005035810 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/376 `/scratch/stefan/7916117/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(C(=O)NCCC1=NC(=O)O[N-]1)C(C)C) `REAL250005035810.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035810 none CCCCCC(C(=O)NCCC1=NC(=O)O[N-]1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 182, 145, 125, 110, 43, 43, 43, 17, 7, 1, 1, 1, 1, 1, 1, 1, 110, 126, 128, 200, 200, 200, 200, 200, 182, 182, 145, 145, 125, 125, 110, 43, 17, 17, 7, 7, 128, 128, 128, 128, 128, 128, 128] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 1022 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035810 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035810 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035810/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035810 Building REAL250005035811 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035811' /scratch/stefan/7916117/working/building/REAL250005035811 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035811 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035811/0 /scratch/stefan/7916117/working/building/REAL250005035811 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/377 `/scratch/stefan/7916117/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(F)C=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035811.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035811 none COC1=C(F)C=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 182, 182, 182, 182, 182, 182, 182, 182, 66, 66, 66, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 182, 182, 66, 21, 21, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035811 none COC1=C(F)C=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 15, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 68, 81, 182, 182, 182, 182, 182, 6, 6, 6, 1, 1, 12, 68, 68, 81, 81] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 465 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035811 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035811 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035811/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035811 Building REAL250005035812 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035812' /scratch/stefan/7916117/working/building/REAL250005035812 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035812 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035812/0 /scratch/stefan/7916117/working/building/REAL250005035812 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/378 `/scratch/stefan/7916117/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1C1CCCC1) `REAL250005035812.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035812 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 68, 171, 171, 171, 171, 171, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 11, 48, 48, 68, 68, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 429 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035812 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 78, 22, 8, 1, 1, 1, 1, 1, 1, 1, 78, 171, 171, 171, 171, 171, 201, 201, 201, 201, 77, 23, 23, 8, 8, 171, 171, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 498 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035812 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 88, 108, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 26, 88, 88, 108, 108, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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, 14, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 561 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035812 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035812 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035812/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035812 Building REAL250005035813 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035813' /scratch/stefan/7916117/working/building/REAL250005035813 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035813 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035813/0 /scratch/stefan/7916117/working/building/REAL250005035813 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/379 `/scratch/stefan/7916117/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1N=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035813.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035813 none CC(C)N1N=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 90, 90, 90, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 25, 25, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 443 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035813 none CC(C)N1N=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 51, 70, 201, 201, 201, 201, 201, 6, 6, 6, 6, 6, 6, 6, 1, 1, 10, 51, 51, 70, 70] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 26, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 479 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035813 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035813 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035813/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035813 Building REAL250005035814 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035814' /scratch/stefan/7916117/working/building/REAL250005035814 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035814 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035814/0 /scratch/stefan/7916117/working/building/REAL250005035814 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/380 `/scratch/stefan/7916117/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NC=C1) `REAL250005035814.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035814 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 41, 67, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 67, 67, 1, 1, 1, 1] 134 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 397 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035814 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 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: [75, 75, 21, 8, 1, 1, 1, 1, 1, 1, 1, 75, 134, 134, 134, 134, 134, 134, 75, 22, 22, 8, 8, 134, 134, 134, 134] 134 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035814 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035814 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035814/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035814 Building REAL250005035815 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035815' /scratch/stefan/7916117/working/building/REAL250005035815 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035815 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035815/0 /scratch/stefan/7916117/working/building/REAL250005035815 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/381 `/scratch/stefan/7916117/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1) `REAL250005035815.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035815 none CCOCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 171, 131, 122, 45, 45, 45, 8, 8, 1, 1, 1, 1, 1, 1, 1, 122, 122, 122, 201, 201, 201, 201, 201, 171, 171, 131, 131, 44, 8, 8, 8, 8, 122, 122, 122, 122, 122, 122] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 714 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035815 none CCOCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 8, 6, 1, 1, 1, 6, 6, 6, 25, 25, 122, 122, 122, 122, 122, 1, 1, 1, 27, 27, 27, 27, 27, 8, 8, 6, 6, 6, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 4, 5, 6, 39, 17, 18, 19, 36, 38, 37] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035815 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035815 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035815/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035815 Building REAL250005035816 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035816' /scratch/stefan/7916117/working/building/REAL250005035816 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035816 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035816/0 /scratch/stefan/7916117/working/building/REAL250005035816 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/382 `/scratch/stefan/7916117/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005035816.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035816 none CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 95, 95, 95, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 24, 24, 8, 8, 201, 200, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL250005035816 none CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 80, 112, 200, 200, 200, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 80, 80, 112, 112, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035816 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035816 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035816/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035816 Building REAL250005035817 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035817' /scratch/stefan/7916117/working/building/REAL250005035817 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035817 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035817/0 /scratch/stefan/7916117/working/building/REAL250005035817 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/383 `/scratch/stefan/7916117/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035817.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035817 none CCC1=CC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 138, 138, 138, 119, 138, 138, 72, 72, 72, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 138, 128, 138, 138, 72, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 785 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035817 none CCC1=CC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 53, 138, 138, 138, 138, 138, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 43, 43, 53, 53] 201 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: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035817 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035817 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035817/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035817 Building REAL250005035818 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035818' /scratch/stefan/7916117/working/building/REAL250005035818 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035818 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035818/0 /scratch/stefan/7916117/working/building/REAL250005035818 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/384 `/scratch/stefan/7916117/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1F) `REAL250005035818.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035818 none COC1=CC=C(F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 174, 174, 174, 174, 174, 174, 51, 51, 51, 20, 8, 1, 1, 1, 1, 1, 1, 1, 174, 174, 201, 201, 201, 174, 174, 51, 20, 20, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 391 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035818 none COC1=CC=C(F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 63, 67, 174, 174, 174, 174, 174, 1, 1, 4, 4, 4, 1, 1, 12, 63, 63, 67, 67] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 24, 25] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035818 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035818 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035818/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035818 Building REAL250005035819 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035819' /scratch/stefan/7916117/working/building/REAL250005035819 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035819 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035819/0 /scratch/stefan/7916117/working/building/REAL250005035819 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/385 `/scratch/stefan/7916117/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)N1N=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035819.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035819 none CCC(CC)N1N=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [186, 162, 137, 162, 185, 137, 137, 137, 137, 60, 60, 60, 19, 8, 1, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 162, 185, 185, 185, 185, 185, 137, 137, 59, 20, 20, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL250005035819 none CCC(CC)N1N=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 4, 6, 1, 1, 1, 1, 1, 1, 10, 10, 10, 44, 50, 137, 137, 137, 137, 137, 7, 7, 7, 7, 7, 4, 6, 6, 6, 6, 6, 1, 1, 10, 44, 44, 50, 50] 201 rigid atoms, others: [32, 33, 2, 5, 6, 7, 8, 9, 10] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 353 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035819 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035819 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035819/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035819 Building REAL250005035820 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035820' /scratch/stefan/7916117/working/building/REAL250005035820 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035820 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035820/0 /scratch/stefan/7916117/working/building/REAL250005035820 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/386 `/scratch/stefan/7916117/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=NC=CN21) `REAL250005035820.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035820 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=NC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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, 1, 12, 12, 59, 93, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 59, 59, 93, 93, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 560 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: REAL250005035820 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=NC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [106, 106, 24, 8, 1, 1, 1, 1, 1, 1, 1, 106, 201, 201, 201, 201, 201, 201, 201, 201, 106, 24, 24, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 459 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035820 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035820 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035820/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035820 Building REAL250005035821 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035821' /scratch/stefan/7916117/working/building/REAL250005035821 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035821 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035821/0 /scratch/stefan/7916117/working/building/REAL250005035821 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/387 `/scratch/stefan/7916117/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC=CC=N1) `REAL250005035821.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035821 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 11, 49, 49, 118, 122, 201, 201, 201, 201, 201, 1, 11, 11, 1, 1, 1, 1, 1, 1, 49, 118, 118, 122, 122, 1, 1, 1, 1] 201 rigid atoms, others: [11, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24]) total number of confs: 602 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035821 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 18, 8, 1, 1, 1, 1, 1, 1, 1, 57, 147, 147, 147, 201, 201, 201, 201, 201, 57, 18, 18, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 668 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035821 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035821 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035821/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035821 Building REAL250005035822 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035822' /scratch/stefan/7916117/working/building/REAL250005035822 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035822 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035822/0 /scratch/stefan/7916117/working/building/REAL250005035822 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/388 `/scratch/stefan/7916117/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=NNC=C21) `REAL250005035822.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035822 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=NNC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 1, 11, 11, 55, 83, 179, 179, 179, 179, 179, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 55, 55, 83, 83, 1, 1, 1, 1, 1, 1, 1, 1, 1] 179 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 497 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: REAL250005035822 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=NNC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 8, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 91, 179, 179, 179, 179, 179, 179, 179, 179, 90, 25, 25, 8, 8, 179, 179, 179, 179, 179, 179, 179, 179, 179] 179 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 558 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035822 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035822/1 /scratch/stefan/7916117/working/building/REAL250005035822 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/389 `/scratch/stefan/7916117/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=C1C=NN2) `REAL250005035822.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035822 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=C1C=NN2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 57, 88, 179, 179, 179, 179, 179, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 57, 57, 88, 88, 1, 1, 1, 1, 1, 1, 1, 1, 1] 179 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 513 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: REAL250005035822 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=C1C=NN2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 92, 179, 179, 179, 179, 179, 179, 179, 179, 92, 24, 24, 8, 8, 179, 179, 179, 179, 179, 179, 179, 179, 179] 179 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 559 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035822 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035822 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035822/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035822/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035822 Building REAL250005035823 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035823' /scratch/stefan/7916117/working/building/REAL250005035823 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035823 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035823/0 /scratch/stefan/7916117/working/building/REAL250005035823 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/390 `/scratch/stefan/7916117/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005035823.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035823 none COC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [201, 201, 161, 201, 161, 161, 161, 83, 83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 161, 201, 201, 201, 161, 161, 82, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 544 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035823 none COC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [9, 9, 1, 9, 1, 1, 1, 1, 1, 10, 10, 10, 44, 65, 161, 161, 161, 161, 161, 1, 10, 10, 10, 1, 1, 10, 44, 44, 65, 65] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 19, 23, 24] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035823 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035823 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035823/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035823 Building REAL250005035824 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035824' /scratch/stefan/7916117/working/building/REAL250005035824 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035824 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035824/0 /scratch/stefan/7916117/working/building/REAL250005035824 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/391 `/scratch/stefan/7916117/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1F) `REAL250005035824.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035824 none CC1=CC(F)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 101, 102, 102, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 101, 22, 22, 8, 8, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 457 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035824 none CC1=CC(F)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 76, 117, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 12, 76, 76, 117, 117, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 23, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 629 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035824 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035824 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035824/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035824 Building REAL250005035825 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035825' /scratch/stefan/7916117/working/building/REAL250005035825 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035825 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035825/0 /scratch/stefan/7916117/working/building/REAL250005035825 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/392 `/scratch/stefan/7916117/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC([N+](=O)[O-])=C1[O-]) `REAL250005035825.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035825 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC([N+](=O)[O-])=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 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: [6, 1, 6, 6, 14, 14, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 1, 1, 1] 25 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) 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: REAL250005035825 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC([N+](=O)[O-])=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 25, 25, 25] 25 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035825 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035825 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035825/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035825 Building REAL250005035826 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035826' /scratch/stefan/7916117/working/building/REAL250005035826 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035826 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035826/0 /scratch/stefan/7916117/working/building/REAL250005035826 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/393 `/scratch/stefan/7916117/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)N1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005035826.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035826 none CCC(CC)N1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [200, 157, 111, 157, 200, 111, 111, 111, 83, 83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 111, 200, 200, 200, 200, 200, 157, 200, 200, 200, 200, 200, 111, 111, 83, 24, 24, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035826 none CCC(CC)N1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 5, 1, 5, 7, 1, 1, 1, 1, 1, 5, 5, 5, 20, 30, 111, 111, 111, 111, 111, 1, 7, 7, 7, 7, 7, 5, 7, 7, 7, 7, 7, 1, 1, 5, 20, 20, 30, 30] 201 rigid atoms, others: [32, 33, 2, 5, 6, 7, 8, 9, 20] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035826 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035826 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035826/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035826 Building REAL250005035827 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035827' /scratch/stefan/7916117/working/building/REAL250005035827 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035827 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035827/0 /scratch/stefan/7916117/working/building/REAL250005035827 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/394 `/scratch/stefan/7916117/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCNC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005035827.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035827 none C=CCNC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 128, 82, 82, 82, 82, 51, 51, 51, 17, 8, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 128, 82, 51, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 749 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035827 none C=CCNC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [45, 21, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 27, 82, 82, 82, 82, 82, 1, 45, 45, 45, 21, 21, 6, 1, 6, 25, 25, 27, 27] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 19, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035827 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035827 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035827/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035827 Building REAL250005035828 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035828' /scratch/stefan/7916117/working/building/REAL250005035828 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035828 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035828/0 /scratch/stefan/7916117/working/building/REAL250005035828 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/395 `/scratch/stefan/7916117/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1) `REAL250005035828.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035828 none CC(C)OC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', '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, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 199, 201, 143, 143, 143, 52, 52, 52, 17, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 201, 201, 201, 201, 201, 201, 201, 143, 52, 17, 17, 8, 8, 143, 143] 201 rigid atoms, others: [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]) total number of confs: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035828 none CC(C)OC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', '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, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [16, 6, 16, 1, 1, 1, 1, 1, 5, 5, 5, 28, 31, 143, 143, 143, 143, 143, 1, 1, 1, 17, 17, 17, 16, 16, 16, 16, 1, 5, 28, 28, 31, 31, 1, 1] 201 rigid atoms, others: [35, 34, 3, 4, 5, 6, 7, 18, 19, 20, 28] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035828 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035828 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035828/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035828 Building REAL250005035829 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035829' /scratch/stefan/7916117/working/building/REAL250005035829 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035829 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035829/0 /scratch/stefan/7916117/working/building/REAL250005035829 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/396 `/scratch/stefan/7916117/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005035829.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035829 none CNC(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 87, 53, 53, 53, 23, 8, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 87, 87, 53, 23, 23, 8, 8] 87 rigid atoms, others: [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]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035829 none CNC(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 28, 40, 87, 87, 87, 87, 87, 1, 4, 4, 4, 4, 1, 1, 1, 7, 27, 27, 40, 40] 87 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 20, 25, 26, 27] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035829 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035829 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035829/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035829 Building REAL250005035830 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035830' /scratch/stefan/7916117/working/building/REAL250005035830 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035830 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035830/0 /scratch/stefan/7916117/working/building/REAL250005035830 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/397 `/scratch/stefan/7916117/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1) `REAL250005035830.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035830 none CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 170, 201, 171, 128, 26, 26, 26, 15, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128, 26, 15, 15, 8, 8, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 811 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035830 none CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 6, 35, 35, 35, 119, 119, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 35, 119, 119, 119, 119, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 17, 18, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035830 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035830 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035830/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035830 Building REAL250005035831 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035831' /scratch/stefan/7916117/working/building/REAL250005035831 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035831 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035831/0 /scratch/stefan/7916117/working/building/REAL250005035831 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/398 `/scratch/stefan/7916117/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC([O-])=CC([N+](=O)[O-])=C1) `REAL250005035831.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035831 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC([O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 1, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 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: [7, 1, 7, 7, 29, 39, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 29, 29, 39, 39, 1, 1, 1] 94 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035831 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC([O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 1, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 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, 54, 20, 8, 1, 1, 1, 1, 1, 1, 1, 55, 94, 94, 94, 94, 94, 94, 94, 94, 94, 54, 20, 20, 8, 8, 94, 94, 94] 94 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035831 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035831/1 /scratch/stefan/7916117/working/building/REAL250005035831 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/399 `/scratch/stefan/7916117/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(O)=CC([N+](=O)[O-])=C1) `REAL250005035831.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035831 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(O)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 1, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 284 conformations in input total number of sets (complete confs): 284 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 33, 56, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 33, 33, 56, 56, 1, 2, 1, 1] 284 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 27]) total number of confs: 367 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035831 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(O)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 1, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 284 conformations in input total number of sets (complete confs): 284 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 22, 8, 1, 1, 1, 1, 1, 1, 1, 82, 142, 142, 142, 142, 142, 142, 142, 142, 142, 81, 22, 22, 8, 8, 142, 284, 142, 142] 284 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035831 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035831 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035831/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035831/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035831 Building REAL250005035832 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035832' /scratch/stefan/7916117/working/building/REAL250005035832 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035832 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035832/0 /scratch/stefan/7916117/working/building/REAL250005035832 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/400 `/scratch/stefan/7916117/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1) `REAL250005035832.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035832 none N#CC1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 127, 73, 73, 73, 24, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 72, 24, 24, 8, 8, 127] 127 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035832 none N#CC1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 59, 127, 127, 127, 127, 127, 1, 1, 1, 1, 7, 37, 37, 59, 59, 1] 127 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035832 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035832 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035832/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035832 Building REAL250005035833 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035833' /scratch/stefan/7916117/working/building/REAL250005035833 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035833 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035833/0 /scratch/stefan/7916117/working/building/REAL250005035833 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/401 `/scratch/stefan/7916117/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C(Cl)=C1) `REAL250005035833.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035833 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [7, 1, 7, 7, 42, 69, 129, 129, 129, 129, 129, 1, 1, 1, 1, 1, 1, 1, 1, 7, 42, 42, 69, 69, 1, 1, 1] 129 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005035833 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [56, 56, 21, 8, 1, 1, 1, 1, 1, 1, 1, 56, 129, 129, 129, 129, 129, 129, 129, 56, 21, 21, 8, 8, 129, 129, 129] 129 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035833 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035833 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035833/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035833 Building REAL250005035834 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035834' /scratch/stefan/7916117/working/building/REAL250005035834 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035834 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035834/0 /scratch/stefan/7916117/working/building/REAL250005035834 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/402 `/scratch/stefan/7916117/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(F)=C1) `REAL250005035834.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035834 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 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, 1, 7, 7, 39, 66, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 66, 66, 1, 1, 1] 132 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) 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: REAL250005035834 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 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: [62, 62, 21, 8, 1, 1, 1, 1, 1, 1, 1, 62, 132, 132, 132, 132, 132, 132, 62, 21, 21, 8, 8, 132, 132, 132] 132 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035834 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035834 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035834/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035834 Building REAL250005035835 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035835' /scratch/stefan/7916117/working/building/REAL250005035835 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035835 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035835/0 /scratch/stefan/7916117/working/building/REAL250005035835 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/403 `/scratch/stefan/7916117/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1) `REAL250005035835.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035835 none CCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 185, 66, 66, 66, 19, 8, 1, 1, 1, 1, 1, 1, 1, 185, 185, 185, 201, 201, 201, 201, 201, 201, 201, 66, 19, 19, 8, 8, 185, 185, 185, 185, 185, 185] 201 rigid atoms, others: [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, 33, 34, 35]) total number of confs: 644 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035835 none CCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 1, 1, 1, 7, 7, 7, 37, 61, 185, 185, 185, 185, 185, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 37, 37, 61, 61, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 34, 15, 16, 17, 35, 30, 31] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035835 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035835 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035835/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035835 Building REAL250005035836 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035836' /scratch/stefan/7916117/working/building/REAL250005035836 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035836 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035836/0 /scratch/stefan/7916117/working/building/REAL250005035836 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/404 `/scratch/stefan/7916117/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)NC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035836.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035836 none CC1=CC(=O)NC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 158, 158, 158, 93, 93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 158, 158, 93, 24, 24, 8, 8] 158 rigid atoms, others: [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]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035836 none CC1=CC(=O)NC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 57, 86, 158, 158, 158, 158, 158, 2, 2, 2, 1, 1, 1, 10, 57, 57, 86, 86] 158 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035836 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035836 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035836/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035836 Building REAL250005035837 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035837' /scratch/stefan/7916117/working/building/REAL250005035837 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035837 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035837/0 /scratch/stefan/7916117/working/building/REAL250005035837 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/405 `/scratch/stefan/7916117/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035837.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035837 none COC1=CC=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 195, 195, 195, 112, 195, 195, 195, 61, 61, 61, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 195, 195, 61, 20, 20, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035837 none COC1=CC=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 65, 77, 195, 195, 195, 195, 195, 4, 4, 4, 1, 1, 1, 13, 65, 65, 77, 77] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035837 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035837 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035837/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035837 Building REAL250005035838 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035838' /scratch/stefan/7916117/working/building/REAL250005035838 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035838 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035838/0 /scratch/stefan/7916117/working/building/REAL250005035838 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/406 `/scratch/stefan/7916117/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035838.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035838 none CC1=CC=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 187, 187, 187, 187, 103, 103, 103, 24, 8, 1, 1, 1, 1, 1, 1, 1, 187, 187, 187, 187, 187, 187, 103, 24, 24, 8, 8] 187 rigid atoms, others: [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]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035838 none CC1=CC=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 58, 95, 187, 187, 187, 187, 187, 2, 2, 2, 1, 1, 1, 9, 58, 58, 95, 95] 187 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035838 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035838 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035838/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035838 Building REAL250005035839 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035839' /scratch/stefan/7916117/working/building/REAL250005035839 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035839 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035839/0 /scratch/stefan/7916117/working/building/REAL250005035839 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/407 `/scratch/stefan/7916117/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[NH+](CC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005035839.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035839 none CC1CC[NH+](CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 145, 157, 65, 65, 65, 17, 8, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157, 145, 145, 65, 17, 17, 8, 8, 157, 157, 157, 157] 157 rigid atoms, others: [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, 36, 37, 38]) 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: REAL250005035839 none CC1CC[NH+](CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 21, 21, 21, 59, 73, 157, 157, 157, 157, 157, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 21, 59, 59, 73, 73, 1, 1, 1, 1] 157 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 18, 19, 23, 24, 25, 26, 27, 36, 37, 35] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035839 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035839/1 /scratch/stefan/7916117/working/building/REAL250005035839 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/408 `/scratch/stefan/7916117/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(CC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005035839.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035839 none CC1CCN(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 166, 58, 58, 58, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 166, 166, 57, 20, 20, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 707 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035839 none CC1CCN(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 23, 23, 23, 89, 98, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 6, 6, 23, 89, 89, 98, 98, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 17, 18, 35, 22, 23, 24, 25, 26, 37, 36] set([32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 27, 28, 29, 30, 31]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035839 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035839 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035839/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035839/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035839 Building REAL250005035840 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035840' /scratch/stefan/7916117/working/building/REAL250005035840 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035840 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035840/0 /scratch/stefan/7916117/working/building/REAL250005035840 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/409 `/scratch/stefan/7916117/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCNC(=O)C1) `REAL250005035840.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035840 none O=C(NCCC1=NC(=O)O[N-]1)C1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 63, 96, 188, 188, 188, 188, 188, 1, 1, 1, 1, 1, 1, 1, 12, 63, 63, 96, 96, 1, 1, 1, 1, 1, 1, 1, 1] 188 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 551 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: REAL250005035840 none O=C(NCCC1=NC(=O)O[N-]1)C1CCNC(=O)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 11, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 24, 8, 1, 1, 1, 1, 1, 1, 1, 92, 188, 188, 188, 188, 188, 188, 91, 25, 25, 8, 8, 188, 188, 188, 188, 188, 188, 188, 188] 188 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 582 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035840 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035840 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035840/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035840 Building REAL250005035841 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035841' /scratch/stefan/7916117/working/building/REAL250005035841 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035841 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035841/0 /scratch/stefan/7916117/working/building/REAL250005035841 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/410 `/scratch/stefan/7916117/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005035841.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035841 none CC(C)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.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, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 184, 201, 184, 184, 185, 185, 84, 85, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 184, 201, 201, 201, 201, 201, 201, 201, 184, 185, 185, 84, 24, 24, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 524 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035841 none CC(C)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.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, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [5, 1, 5, 1, 1, 1, 1, 1, 1, 11, 11, 11, 45, 62, 185, 185, 185, 184, 184, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 45, 45, 62, 62] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 27, 28, 29] set([0, 2, 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: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035841 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035841 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035841/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035841 Building REAL250005035842 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035842' /scratch/stefan/7916117/working/building/REAL250005035842 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035842 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035842/0 /scratch/stefan/7916117/working/building/REAL250005035842 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/411 `/scratch/stefan/7916117/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035842.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035842 none COC(=O)C(C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 142, 201, 111, 142, 37, 37, 37, 16, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 142, 142, 142, 142, 111, 111, 37, 16, 16, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 827 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035842 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035842 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035842/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035842 Building REAL250005035843 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035843' /scratch/stefan/7916117/working/building/REAL250005035843 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035843 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035843/0 /scratch/stefan/7916117/working/building/REAL250005035843 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/412 `/scratch/stefan/7916117/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(F)C=C1Cl)NCCC1=NC(=O)O[N-]1) `REAL250005035843.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035843 none O=C(CC1=CC=C(F)C=C1Cl)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 16, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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, 33, 33, 125, 201, 201, 201, 201, 201, 201, 201, 15, 8, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 33, 15, 15, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035843 none O=C(CC1=CC=C(F)C=C1Cl)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 1, 16, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 115, 115, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 33, 115, 115, 115, 115] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035843 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035843 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035843/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035843 Building REAL250005035844 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035844' /scratch/stefan/7916117/working/building/REAL250005035844 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035844 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035844/0 /scratch/stefan/7916117/working/building/REAL250005035844 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/413 `/scratch/stefan/7916117/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl) `REAL250005035844.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035844 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 49, 49, 49, 22, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 102, 127, 127, 127, 127, 127, 49, 22, 23, 8, 8, 127, 127] 127 rigid atoms, others: [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]) 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: REAL250005035844 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 7, 7, 7, 41, 63, 127, 127, 127, 127, 127, 1, 1, 1, 1, 2, 2, 2, 1, 7, 41, 41, 63, 63, 1, 1] 127 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 22, 28, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035844 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035844 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035844/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035844 Building REAL250005035845 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035845' /scratch/stefan/7916117/working/building/REAL250005035845 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035845 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035845/0 /scratch/stefan/7916117/working/building/REAL250005035845 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/414 `/scratch/stefan/7916117/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035845.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035845 none CC1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 170, 56, 56, 56, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 170, 56, 19, 19, 8, 8, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 781 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035845 none CC1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 5, 28, 28, 28, 105, 107, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 28, 105, 105, 107, 107, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 17, 35, 21, 22, 23, 24, 25, 26] set([32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035845 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035845 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035845/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035845 Building REAL250005035846 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035846' /scratch/stefan/7916117/working/building/REAL250005035846 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035846 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035846/0 /scratch/stefan/7916117/working/building/REAL250005035846 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/415 `/scratch/stefan/7916117/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCSCC1)NCCC1=NC(=O)O[N-]1) `REAL250005035846.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035846 none O=C(CC1CCSCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 14, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [54, 54, 54, 172, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 172, 172, 201, 201, 201, 201, 201, 201, 201, 201, 201, 54, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 753 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035846 none O=C(CC1CCSCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 14, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [25, 6, 1, 1, 1, 1, 1, 1, 1, 25, 25, 104, 110, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 104, 104, 110, 110] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 568 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035846 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035846 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035846/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035846 Building REAL250005035847 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035847' /scratch/stefan/7916117/working/building/REAL250005035847 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035847 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035847/0 /scratch/stefan/7916117/working/building/REAL250005035847 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/416 `/scratch/stefan/7916117/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(=CC(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035847.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035847 none CC1CCC(=CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 193, 193, 100, 100, 100, 24, 8, 1, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 193, 193, 193, 193, 193, 99, 24, 24, 8, 8, 193, 193] 193 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL250005035847 none CC1CCC(=CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 53, 75, 193, 193, 193, 193, 193, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 53, 53, 75, 75, 1, 1] 193 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 17, 21, 22, 23, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 27, 28, 29, 30, 31]) total number of confs: 490 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035847 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035847 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035847/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035847 Building REAL250005035848 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035848' /scratch/stefan/7916117/working/building/REAL250005035848 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035848 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035848/0 /scratch/stefan/7916117/working/building/REAL250005035848 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/417 `/scratch/stefan/7916117/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035848.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035848 none CCC(OC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 101, 46, 101, 150, 179, 179, 179, 179, 179, 46, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 101, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 45, 8, 8, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 845 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035848 none CCC(OC1CCCCC1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 1, 1, 1, 1, 1, 1, 1, 12, 33, 33, 33, 100, 100, 179, 179, 179, 179, 179, 27, 27, 27, 27, 27, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 100, 100, 100, 100] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 37, 35, 36, 27, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 38, 39, 40, 41, 42]) total number of confs: 585 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035848 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035848 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035848/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035848 Building REAL250005035849 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035849' /scratch/stefan/7916117/working/building/REAL250005035849 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035849 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035849/0 /scratch/stefan/7916117/working/building/REAL250005035849 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/418 `/scratch/stefan/7916117/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(CC(=O)NCCC1=NC(=O)O[N-]1)C(C)C) `REAL250005035849.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035849 none CCOC(CC(=O)NCCC1=NC(=O)O[N-]1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 161, 157, 146, 47, 47, 47, 19, 7, 1, 1, 1, 1, 1, 1, 1, 157, 173, 173, 187, 187, 187, 187, 187, 157, 146, 146, 47, 19, 19, 7, 7, 173, 173, 173, 173, 173, 173, 173] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 892 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035849 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035849 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035849/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035849 Building REAL250005035850 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035850' /scratch/stefan/7916117/working/building/REAL250005035850 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035850 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035850/0 /scratch/stefan/7916117/working/building/REAL250005035850 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/419 `/scratch/stefan/7916117/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1) `REAL250005035850.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035850 none COCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 166, 146, 78, 78, 78, 19, 8, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 201, 201, 201, 178, 178, 166, 166, 77, 19, 19, 8, 8, 146, 146, 146, 146, 146, 146, 146, 146] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 731 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: REAL250005035850 none COCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 4, 4, 4, 19, 31, 146, 146, 146, 146, 146, 1, 1, 1, 1, 17, 17, 17, 7, 7, 6, 6, 4, 19, 19, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 35, 39, 16, 17, 18, 19, 36, 38, 37] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 311 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035850 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035850 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035850/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035850 Building REAL250005035851 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035851' /scratch/stefan/7916117/working/building/REAL250005035851 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035851 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035851/0 /scratch/stefan/7916117/working/building/REAL250005035851 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/420 `/scratch/stefan/7916117/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(C)(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035851.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035851 none CC1=CC=CC=C1C(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 82, 201, 201, 82, 82, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 23, 24, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 753 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: REAL250005035851 none CC1=CC=CC=C1C(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 5, 5, 5, 11, 11, 11, 61, 80, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 11, 61, 61, 80, 80] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 524 number of broken/clashed sets: 128 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035851 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035851 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035851/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035851 Building REAL250005035852 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035852' /scratch/stefan/7916117/working/building/REAL250005035852 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035852 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035852/0 /scratch/stefan/7916117/working/building/REAL250005035852 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/421 `/scratch/stefan/7916117/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1) `REAL250005035852.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035852 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 21, 21, 21, 84, 93, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 21, 84, 84, 93, 93, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 539 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035852 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 53, 164, 53, 53, 19, 8, 1, 1, 1, 1, 1, 1, 1, 164, 201, 201, 164, 201, 201, 201, 164, 164, 164, 164, 164, 164, 53, 19, 19, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 880 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035852 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035852 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035852/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035852 Building REAL250005035853 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035853' /scratch/stefan/7916117/working/building/REAL250005035853 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035853 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035853/0 /scratch/stefan/7916117/working/building/REAL250005035853 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/422 `/scratch/stefan/7916117/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035853.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035853 none CC1=CC=C(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 160, 48, 160, 160, 48, 48, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 160, 160, 47, 18, 17, 8, 8, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL250005035853 none CC1=CC=C(C(C)(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 26, 26, 26, 88, 100, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10, 10, 10, 10, 26, 88, 88, 100, 100, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 19, 20, 24, 25, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035853 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035853 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035853/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035853 Building REAL250005035854 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035854' /scratch/stefan/7916117/working/building/REAL250005035854 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035854 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035854/0 /scratch/stefan/7916117/working/building/REAL250005035854 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/423 `/scratch/stefan/7916117/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1) `REAL250005035854.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035854 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 33, 33, 33, 95, 101, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 33, 95, 95, 101, 101, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 568 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035854 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 121, 45, 45, 15, 7, 1, 1, 1, 1, 1, 1, 1, 121, 201, 201, 201, 201, 201, 201, 121, 121, 121, 121, 121, 121, 45, 15, 15, 7, 7, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 611 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035854 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035854 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035854/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035854 Building REAL250005035855 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035855' /scratch/stefan/7916117/working/building/REAL250005035855 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035855 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035855/0 /scratch/stefan/7916117/working/building/REAL250005035855 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/424 `/scratch/stefan/7916117/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)[NH+](C)C) `REAL250005035855.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035855 none CC(C)[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 1, 7, 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: [53, 62, 63, 38, 62, 38, 38, 17, 8, 1, 1, 1, 1, 1, 1, 1, 62, 63, 63, 62, 63, 63, 63, 63, 63, 63, 63, 38, 17, 17, 8, 8, 63, 63, 63, 63, 63, 63] 63 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 355 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035855 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035855 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035855/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035855 Building REAL250005035856 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035856' /scratch/stefan/7916117/working/building/REAL250005035856 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035856 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035856/0 /scratch/stefan/7916117/working/building/REAL250005035856 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/425 `/scratch/stefan/7916117/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)(CCC)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035856.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035856 none CCCC(O)(CCC)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [197, 197, 148, 112, 148, 141, 182, 182, 45, 45, 45, 17, 8, 1, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 197, 197, 444, 182, 177, 182, 182, 182, 182, 182, 112, 112, 45, 17, 17, 8, 8] 603 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1519 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035856 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035856 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035856/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035856 Building REAL250005035857 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035857' /scratch/stefan/7916117/working/building/REAL250005035857 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035857 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035857/0 /scratch/stefan/7916117/working/building/REAL250005035857 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/426 `/scratch/stefan/7916117/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035857.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035857 none COC(=O)CC(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 33, 55, 31, 22, 31, 22, 22, 12, 7, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 33, 33, 31, 31, 31, 31, 22, 12, 12, 7, 7] 55 rigid atoms, others: [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]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035857 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035857 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035857/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035857 Building REAL250005035858 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035858' /scratch/stefan/7916117/working/building/REAL250005035858 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035858 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035858/0 /scratch/stefan/7916117/working/building/REAL250005035858 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/427 `/scratch/stefan/7916117/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)OC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035858.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035858 none CC1=C(C)OC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 151, 151, 82, 82, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 151, 151, 82, 24, 24, 8, 8, 151] 151 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL250005035858 none CC1=C(C)OC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 66, 93, 151, 151, 151, 151, 151, 1, 2, 2, 2, 2, 2, 2, 13, 66, 66, 93, 93, 1] 151 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 496 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035858 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035858 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035858/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035858 Building REAL250005035859 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035859' /scratch/stefan/7916117/working/building/REAL250005035859 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035859 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035859/0 /scratch/stefan/7916117/working/building/REAL250005035859 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/428 `/scratch/stefan/7916117/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(CC=C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035859.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035859 none C=CCC(CC=C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [184, 144, 98, 37, 100, 139, 175, 37, 37, 8, 8, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 144, 144, 100, 139, 139, 175, 175, 175, 36, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 1145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035859 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035859 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035859/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035859 Building REAL250005035860 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035860' /scratch/stefan/7916117/working/building/REAL250005035860 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035860 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035860/0 /scratch/stefan/7916117/working/building/REAL250005035860 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/429 `/scratch/stefan/7916117/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)N1) `REAL250005035860.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035860 none CC1=CC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 171, 171, 89, 89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 171, 171, 171, 171, 89, 24, 24, 8, 8, 171] 171 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 401 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: REAL250005035860 none CC1=CC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 71, 97, 171, 171, 171, 171, 171, 1, 2, 2, 2, 1, 2, 2, 2, 12, 71, 71, 97, 97, 1] 171 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 21, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 509 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035860 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035860 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035860/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035860 Building REAL250005035861 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035861' /scratch/stefan/7916117/working/building/REAL250005035861 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035861 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035861/0 /scratch/stefan/7916117/working/building/REAL250005035861 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/430 `/scratch/stefan/7916117/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2SC=CC2=C1) `REAL250005035861.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035861 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2SC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 37, 62, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 62, 62, 1, 1, 1, 1, 1] 124 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) 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: REAL250005035861 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2SC=CC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 14, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 21, 8, 1, 1, 1, 1, 1, 1, 1, 53, 124, 124, 124, 124, 124, 124, 124, 124, 52, 21, 21, 8, 8, 124, 124, 124, 124, 124] 124 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035861 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035861 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035861/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035861 Building REAL250005035862 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035862' /scratch/stefan/7916117/working/building/REAL250005035862 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035862 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035862/0 /scratch/stefan/7916117/working/building/REAL250005035862 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/431 `/scratch/stefan/7916117/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1CCCCCC1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035862.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035862 none CC(OC1CCCCCC1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 57, 145, 190, 201, 201, 201, 201, 201, 201, 57, 57, 17, 7, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 57, 17, 17, 7, 7] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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: REAL250005035862 none CC(OC1CCCCCC1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 9, 34, 34, 34, 112, 117, 201, 201, 201, 201, 201, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 112, 112, 117, 117] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 36, 34, 37, 35, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 38, 39, 40, 41, 42]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035862 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035862 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035862/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035862 Building REAL250005035863 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035863' /scratch/stefan/7916117/working/building/REAL250005035863 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035863 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035863/0 /scratch/stefan/7916117/working/building/REAL250005035863 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/432 `/scratch/stefan/7916117/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2CC2)S1) `REAL250005035863.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035863 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2CC2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 13, 13, 1, 9, 38, 38, 48, 48, 1, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035863 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2CC2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 20, 8, 1, 1, 1, 1, 1, 1, 1, 63, 105, 105, 105, 105, 201, 201, 105, 63, 20, 20, 8, 8, 105, 105, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035863 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2CC2)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 46, 46, 117, 130, 201, 201, 201, 201, 201, 13, 13, 13, 1, 1, 1, 1, 13, 46, 117, 117, 130, 130, 13, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [14, 15, 16, 17, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 606 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035863 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035863 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035863/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035863 Building REAL250005035864 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035864' /scratch/stefan/7916117/working/building/REAL250005035864 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035864 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035864/0 /scratch/stefan/7916117/working/building/REAL250005035864 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/433 `/scratch/stefan/7916117/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C=CC=C1O) `REAL250005035864.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035864/0/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: REAL250005035864 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C=CC=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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: [7, 1, 7, 7, 31, 35, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 7, 31, 31, 35, 35, 2, 1, 1, 1, 2] 268 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 187 number of broken/clashed sets: 64 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035864 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C=CC=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 4, 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: [38, 38, 21, 8, 1, 1, 1, 1, 1, 1, 1, 38, 67, 67, 67, 66, 67, 67, 67, 37, 22, 21, 8, 8, 134, 67, 66, 67, 134] 268 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 467 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035864 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035864 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035864/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035864 Building REAL250005035865 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035865' /scratch/stefan/7916117/working/building/REAL250005035865 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035865 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035865/0 /scratch/stefan/7916117/working/building/REAL250005035865 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/434 `/scratch/stefan/7916117/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC(Cl)=C1) `REAL250005035865.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035865 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 43, 67, 171, 171, 171, 171, 171, 1, 1, 1, 1, 1, 1, 1, 1, 7, 43, 43, 67, 67, 1, 1, 1] 171 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005035865 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(F)=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [65, 65, 20, 8, 1, 1, 1, 1, 1, 1, 1, 65, 171, 171, 171, 171, 171, 171, 171, 65, 20, 20, 8, 8, 171, 171, 171] 171 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035865 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035865 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035865/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035865 Building REAL250005035866 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035866' /scratch/stefan/7916117/working/building/REAL250005035866 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035866 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035866/0 /scratch/stefan/7916117/working/building/REAL250005035866 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/435 `/scratch/stefan/7916117/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCC(C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005035866.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035866 none CCC1CCC(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 144, 144, 144, 144, 77, 77, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 144, 201, 201, 201, 201, 201, 144, 144, 144, 144, 144, 144, 77, 24, 24, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 801 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035866 none CCC1CCC(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 56, 70, 144, 144, 144, 144, 144, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 11, 56, 56, 70, 70] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 23, 24, 25, 26, 27, 28] set([0, 32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035866 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035866 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035866/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035866 Building REAL250005035867 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035867' /scratch/stefan/7916117/working/building/REAL250005035867 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035867 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035867/0 /scratch/stefan/7916117/working/building/REAL250005035867 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/436 `/scratch/stefan/7916117/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN=C2NC=CC=C12)NCCC1=NC(=O)O[N-]1) `REAL250005035867.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035867 none O=C(CC1=CN=C2NC=CC=C12)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 114, 201, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 114, 114, 201, 201, 201, 201, 201, 40, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 574 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035867 none O=C(CC1=CN=C2NC=CC=C12)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 105, 107, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 34, 105, 105, 107, 107] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27] set([0, 1, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035867 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035867 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035867/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035867 Building REAL250005035868 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035868' /scratch/stefan/7916117/working/building/REAL250005035868 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035868 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035868/0 /scratch/stefan/7916117/working/building/REAL250005035868 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/437 `/scratch/stefan/7916117/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1F) `REAL250005035868.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035868 none CC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 196, 201, 201, 102, 102, 102, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 102, 24, 24, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL250005035868 none CC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 72, 107, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 13, 72, 72, 107, 107] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 22, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035868 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035868 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035868/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035868 Building REAL250005035869 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035869' /scratch/stefan/7916117/working/building/REAL250005035869 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035869 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035869/0 /scratch/stefan/7916117/working/building/REAL250005035869 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/438 `/scratch/stefan/7916117/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035869.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035869 none CC(C)OC1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 90, 90, 90, 90, 90, 47, 47, 47, 17, 8, 1, 1, 1, 1, 1, 1, 1, 90, 201, 201, 201, 201, 201, 201, 201, 90, 90, 47, 17, 17, 8, 8, 90] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 407 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035869 none CC(C)OC1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [21, 9, 21, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 25, 90, 90, 90, 90, 90, 1, 21, 21, 21, 21, 21, 21, 21, 1, 1, 5, 23, 23, 25, 25, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 35, 20, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035869 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035869 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035869/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035869 Building REAL250005035870 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035870' /scratch/stefan/7916117/working/building/REAL250005035870 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035870 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035870/0 /scratch/stefan/7916117/working/building/REAL250005035870 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/439 `/scratch/stefan/7916117/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C)=C1OCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035870.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035870 none CC1=NN(C)C(C)=C1OCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 179, 103, 33, 33, 33, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 33, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 558 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035870 none CC1=NN(C)C(C)=C1OCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 1, 1, 3, 13, 68, 69, 69, 133, 133, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 69, 133, 133, 133, 133] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 645 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035870 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035870 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035870/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035870 Building REAL250005035871 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035871' /scratch/stefan/7916117/working/building/REAL250005035871 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035871 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035871/0 /scratch/stefan/7916117/working/building/REAL250005035871 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/440 `/scratch/stefan/7916117/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(C1CC1)C1CC1) `REAL250005035871.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035871 none O=C(NCCC1=NC(=O)O[N-]1)C(C1CC1)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 96, 113, 194, 194, 194, 194, 194, 1, 1, 1, 1, 6, 14, 14, 30, 96, 96, 113, 113, 6, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 201 rigid atoms, others: [11, 12, 13, 14, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33]) total number of confs: 604 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035871 none O=C(NCCC1=NC(=O)O[N-]1)C(C1CC1)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 24, 8, 1, 1, 1, 1, 1, 1, 1, 64, 176, 194, 194, 176, 194, 194, 64, 24, 24, 8, 8, 176, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 818 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035871 none O=C(NCCC1=NC(=O)O[N-]1)C(C1CC1)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 95, 111, 194, 194, 194, 194, 194, 1, 6, 14, 14, 1, 1, 1, 31, 95, 95, 111, 111, 6, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 11, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 601 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035871 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035871 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035871/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035871 Building REAL250005035872 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035872' /scratch/stefan/7916117/working/building/REAL250005035872 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035872 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035872/0 /scratch/stefan/7916117/working/building/REAL250005035872 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/441 `/scratch/stefan/7916117/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21) `REAL250005035872.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035872 none CN1C=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 52, 52, 52, 22, 8, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 106, 106, 106, 51, 22, 22, 8, 8, 106, 106] 106 rigid atoms, others: [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]) 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: REAL250005035872 none CN1C=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 35, 58, 106, 106, 106, 106, 106, 1, 1, 1, 2, 2, 2, 1, 1, 7, 35, 35, 58, 58, 1, 1] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 32, 24, 25, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035872 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035872 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035872/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035872 Building REAL250005035873 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035873' /scratch/stefan/7916117/working/building/REAL250005035873 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035873 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035873/0 /scratch/stefan/7916117/working/building/REAL250005035873 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/442 `/scratch/stefan/7916117/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC(Cl)=CC=C1F) `REAL250005035873.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035873 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC(Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 16, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 69, 95, 197, 197, 197, 197, 197, 1, 1, 1, 1, 1, 1, 1, 1, 12, 69, 69, 95, 95, 1, 1] 197 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 541 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035873 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC(Cl)=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 16, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 24, 8, 1, 1, 1, 1, 1, 1, 1, 105, 197, 197, 197, 197, 197, 197, 197, 104, 25, 25, 8, 8, 197, 197] 197 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 454 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035873 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035873 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035873/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035873 Building REAL250005035874 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035874' /scratch/stefan/7916117/working/building/REAL250005035874 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035874 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035874/0 /scratch/stefan/7916117/working/building/REAL250005035874 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/443 `/scratch/stefan/7916117/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C([N+](=O)[O-])C=NN1) `REAL250005035874.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035874 none O=C(NCCC1=NC(=O)O[N-]1)C1=C([N+](=O)[O-])C=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 11, 11, 1, 8, 8, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 4, 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: [12, 1, 12, 12, 65, 99, 192, 192, 192, 192, 192, 1, 1, 1, 2, 2, 1, 1, 1, 12, 65, 65, 99, 99, 1, 1] 192 rigid atoms, others: [1, 11, 12, 13, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 19, 20, 21, 22, 23]) 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: REAL250005035874 none O=C(NCCC1=NC(=O)O[N-]1)C1=C([N+](=O)[O-])C=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 11, 11, 1, 8, 8, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 3, 7, 7, 4, 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: [110, 110, 24, 8, 1, 1, 1, 1, 1, 1, 1, 110, 192, 192, 192, 192, 192, 192, 192, 110, 24, 24, 8, 8, 192, 192] 192 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035874 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035874/1 /scratch/stefan/7916117/working/building/REAL250005035874 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/444 `/scratch/stefan/7916117/working/3D/444' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NNC=C1[N+](=O)[O-]) `REAL250005035874.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035874 none O=C(NCCC1=NC(=O)O[N-]1)C1=NNC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 8, 11, 11, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 62, 92, 197, 197, 197, 197, 197, 1, 1, 1, 1, 1, 1, 2, 2, 11, 62, 62, 92, 92, 1, 1] 197 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23]) 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: REAL250005035874 none O=C(NCCC1=NC(=O)O[N-]1)C1=NNC=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 8, 11, 11, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 24, 8, 1, 1, 1, 1, 1, 1, 1, 101, 197, 197, 197, 197, 197, 197, 197, 100, 25, 25, 8, 8, 197, 197] 197 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035874 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035874 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035874/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035874/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035874 Building REAL250005035875 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035875' /scratch/stefan/7916117/working/building/REAL250005035875 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035875 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035875/0 /scratch/stefan/7916117/working/building/REAL250005035875 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/445 `/scratch/stefan/7916117/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NCCC2=NC(=O)O[N-]2)CCC1=O) `REAL250005035875.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035875 none CC1CC(C(=O)NCCC2=NC(=O)O[N-]2)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 104, 104, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 24, 24, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [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, 33, 34]) total number of confs: 608 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035875 none CC1CC(C(=O)NCCC2=NC(=O)O[N-]2)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 69, 92, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 13, 69, 69, 92, 92, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 15, 16, 17, 18, 22, 23, 24, 25, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 26, 27, 28, 29, 30]) total number of confs: 548 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035875 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035875 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035875/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035875 Building REAL250005035876 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035876' /scratch/stefan/7916117/working/building/REAL250005035876 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035876 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035876/0 /scratch/stefan/7916117/working/building/REAL250005035876 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/446 `/scratch/stefan/7916117/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1C[N@@H+]2CCN1CCC2) `REAL250005035876.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035876 none O=C(NCCC1=NC(=O)O[N-]1)C1C[N@@H+]2CCN1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 9, 6, 5, 5, 10, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 23, 27, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 154 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: REAL250005035876 none O=C(NCCC1=NC(=O)O[N-]1)C1C[N@@H+]2CCN1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 9, 6, 5, 5, 10, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 17, 9, 1, 1, 1, 1, 1, 1, 1, 52, 59, 59, 59, 59, 59, 59, 59, 59, 59, 52, 17, 17, 9, 9, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59] 59 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035876 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035876/1 /scratch/stefan/7916117/working/building/REAL250005035876 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/447 `/scratch/stefan/7916117/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1C[N@H+]2CCN1CCC2) `REAL250005035876.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035876 none O=C(NCCC1=NC(=O)O[N-]1)C1C[N@H+]2CCN1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 9, 6, 5, 5, 10, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 30, 35, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 30, 30, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 76 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 200 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: REAL250005035876 none O=C(NCCC1=NC(=O)O[N-]1)C1C[N@H+]2CCN1CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 9, 6, 5, 5, 10, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 17, 9, 1, 1, 1, 1, 1, 1, 1, 58, 76, 76, 76, 76, 76, 76, 76, 76, 76, 58, 17, 17, 9, 9, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76, 76] 76 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 254 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035876 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035876 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035876/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035876/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035876 Building REAL250005035877 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035877' /scratch/stefan/7916117/working/building/REAL250005035877 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035877 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035877/0 /scratch/stefan/7916117/working/building/REAL250005035877 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/448 `/scratch/stefan/7916117/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NN1CC(C)C) `REAL250005035877.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035877 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NN1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 63, 63, 63, 21, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 201, 201, 201, 128, 128, 128, 63, 21, 21, 8, 8, 128, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 756 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035877 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NN1CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 45, 61, 128, 128, 128, 128, 128, 1, 1, 1, 1, 3, 3, 3, 2, 2, 2, 9, 45, 45, 61, 61, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 357 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035877 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035877 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035877/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035877 Building REAL250005035878 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035878' /scratch/stefan/7916117/working/building/REAL250005035878 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035878 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035878/0 /scratch/stefan/7916117/working/building/REAL250005035878 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/449 `/scratch/stefan/7916117/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F) `REAL250005035878.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035878 none CSC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 147, 147, 147, 53, 53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 201, 201, 201, 147, 53, 17, 17, 8, 8, 147, 147] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 422 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035878 none CSC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [9, 1, 1, 1, 1, 1, 5, 5, 5, 28, 32, 147, 147, 147, 147, 147, 1, 1, 1, 1, 9, 9, 9, 1, 5, 28, 28, 32, 32, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 23, 29, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035878 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035878 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035878/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035878 Building REAL250005035879 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035879' /scratch/stefan/7916117/working/building/REAL250005035879 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035879 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035879/0 /scratch/stefan/7916117/working/building/REAL250005035879 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/450 `/scratch/stefan/7916117/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=S=NC2=C1) `REAL250005035879.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 Warning: Using closest atom type 177 for atom 17 Warning: Using closest atom type 177 for atom 17 ('energy: ', 12.0) ('conf: ', 200) Warning: Using closest atom type 177 for atom 17 Warning: Using closest atom type 177 for atom 17 ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035879 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=S=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 14, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 37, 68, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 68, 68, 1, 1, 1] 125 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035879 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=S=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 14, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 21, 8, 1, 1, 1, 1, 1, 1, 1, 60, 125, 125, 125, 125, 125, 125, 125, 125, 59, 21, 21, 8, 8, 125, 125, 125] 125 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035879 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035879 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035879/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035879 Building REAL250005035880 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035880' /scratch/stefan/7916117/working/building/REAL250005035880 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035880 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035880/0 /scratch/stefan/7916117/working/building/REAL250005035880 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/451 `/scratch/stefan/7916117/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CSCC(F)(F)F)NCCC1=NC(=O)O[N-]1) `REAL250005035880.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035880 none O=C(CSCC(F)(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 14, 5, 5, 15, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [57, 57, 57, 151, 181, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 151, 151, 201, 201, 57, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035880 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035880 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035880/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035880 Building REAL250005035881 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035881' /scratch/stefan/7916117/working/building/REAL250005035881 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035881 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035881/0 /scratch/stefan/7916117/working/building/REAL250005035881 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/452 `/scratch/stefan/7916117/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)NCCC1=NC(=O)O[N-]1)C(C)C) `REAL250005035881.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035881 none CCCC(C(=O)NCCC1=NC(=O)O[N-]1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [170, 161, 128, 46, 46, 46, 8, 8, 1, 1, 1, 1, 1, 1, 1, 123, 148, 148, 170, 170, 170, 166, 170, 165, 165, 128, 45, 9, 9, 8, 8, 148, 148, 148, 148, 148, 148, 148] 172 rigid atoms, others: [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, 33, 34, 35, 36, 37]) total number of confs: 820 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035881 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035881 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035881/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035881 Building REAL250005035882 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035882' /scratch/stefan/7916117/working/building/REAL250005035882 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035882 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035882/0 /scratch/stefan/7916117/working/building/REAL250005035882 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/453 `/scratch/stefan/7916117/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CN=C1) `REAL250005035882.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035882 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 33, 33, 33, 96, 98, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 33, 96, 96, 98, 98, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 553 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035882 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 41, 125, 41, 41, 15, 7, 1, 1, 1, 1, 1, 1, 1, 125, 201, 201, 201, 201, 201, 125, 125, 125, 125, 125, 125, 41, 15, 15, 7, 7, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 623 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035882 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035882 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035882/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035882 Building REAL250005035883 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035883' /scratch/stefan/7916117/working/building/REAL250005035883 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035883 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035883/0 /scratch/stefan/7916117/working/building/REAL250005035883 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/454 `/scratch/stefan/7916117/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NO1) `REAL250005035883.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035883 none CN(C)CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 195, 201, 117, 117, 117, 76, 76, 76, 22, 8, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 201, 195, 195, 117, 75, 23, 23, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035883 none CN(C)CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 1, 1, 1, 1, 1, 7, 7, 7, 26, 36, 117, 117, 117, 117, 117, 1, 1, 13, 13, 13, 13, 13, 13, 7, 7, 1, 7, 26, 26, 36, 36] 201 rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 28] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 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/7916117/working/building/REAL250005035883 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035883/1 /scratch/stefan/7916117/working/building/REAL250005035883 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/455 `/scratch/stefan/7916117/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NO1) `REAL250005035883.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035883 none C[NH+](C)CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 148, 148, 148, 102, 102, 102, 17, 8, 1, 1, 1, 1, 1, 1, 1, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 148, 102, 17, 17, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 686 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035883 none C[NH+](C)CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 10, 10, 1, 1, 1, 1, 1, 6, 6, 6, 24, 35, 148, 148, 148, 148, 148, 1, 1, 10, 10, 10, 10, 10, 10, 7, 7, 1, 6, 24, 24, 35, 35] 201 rigid atoms, others: [4, 5, 6, 7, 8, 19, 20, 29] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035883 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035883 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035883/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035883/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035883 Building REAL250005035884 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035884' /scratch/stefan/7916117/working/building/REAL250005035884 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035884 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035884/0 /scratch/stefan/7916117/working/building/REAL250005035884 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/456 `/scratch/stefan/7916117/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(C)=C1F) `REAL250005035884.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035884 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 49, 49, 49, 20, 8, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 49, 49, 69, 69, 69, 69, 49, 20, 20, 8, 8, 69, 69, 69, 69] 69 rigid atoms, others: [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]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035884 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(C)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 4, 4, 4, 22, 33, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 22, 22, 33, 33, 1, 2, 2, 2] 69 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 23, 29] set([32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035884 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035884 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035884/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035884 Building REAL250005035885 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035885' /scratch/stefan/7916117/working/building/REAL250005035885 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035885 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035885/0 /scratch/stefan/7916117/working/building/REAL250005035885 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/457 `/scratch/stefan/7916117/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035885.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035885 none CC(C)N1C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 197, 201, 201, 201, 201, 201, 82, 82, 82, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 82, 20, 20, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035885 none CC(C)N1C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 73, 201, 201, 201, 201, 201, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 10, 50, 50, 73, 73] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 26, 27, 28] 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]) total number of confs: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035885 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035885 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035885/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035885 Building REAL250005035886 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035886' /scratch/stefan/7916117/working/building/REAL250005035886 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035886 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035886/0 /scratch/stefan/7916117/working/building/REAL250005035886 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/458 `/scratch/stefan/7916117/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(Cl)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035886.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035886 none CC1=CC=C(Cl)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 196, 196, 196, 196, 97, 97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 196, 196, 196, 196, 196, 196, 97, 24, 24, 8, 8] 196 rigid atoms, others: [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]) 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: REAL250005035886 none CC1=CC=C(Cl)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 57, 83, 196, 196, 196, 196, 196, 2, 2, 2, 1, 1, 1, 10, 57, 57, 83, 83] 196 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 526 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035886 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035886 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035886/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035886 Building REAL250005035887 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035887' /scratch/stefan/7916117/working/building/REAL250005035887 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035887 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035887/0 /scratch/stefan/7916117/working/building/REAL250005035887 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/459 `/scratch/stefan/7916117/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(Cl)=C1F) `REAL250005035887.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035887 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(Cl)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 16, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [12, 1, 12, 13, 72, 100, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 13, 72, 72, 100, 100, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 576 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035887 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(Cl)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 16, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [101, 101, 24, 8, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 200, 201, 201, 201, 101, 24, 24, 8, 8, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035887 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035887 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035887/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035887 Building REAL250005035888 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035888' /scratch/stefan/7916117/working/building/REAL250005035888 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035888 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035888/0 /scratch/stefan/7916117/working/building/REAL250005035888 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/460 `/scratch/stefan/7916117/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005035888.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035888 none CC(C)[C@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 200, 162, 162, 162, 162, 54, 162, 54, 54, 19, 8, 1, 1, 1, 1, 1, 1, 1, 162, 162, 201, 201, 201, 201, 201, 200, 201, 162, 162, 162, 162, 54, 19, 19, 8, 8, 162, 162, 162, 162] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 723 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035888 none CC(C)[C@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 55, 69, 162, 162, 162, 162, 162, 1, 1, 8, 8, 8, 7, 8, 8, 8, 1, 1, 1, 1, 12, 55, 55, 69, 69, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 39, 40, 20, 21, 41, 38, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035888 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035888 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035888/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035888 Building REAL250005035889 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035889' /scratch/stefan/7916117/working/building/REAL250005035889 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035889 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035889/0 /scratch/stefan/7916117/working/building/REAL250005035889 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/461 `/scratch/stefan/7916117/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035889.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035889 none CN1C(=O)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 189, 189, 189, 189, 109, 109, 109, 24, 8, 1, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 189, 189, 109, 24, 24, 8, 8] 189 rigid atoms, others: [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]) 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: REAL250005035889 none CN1C(=O)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 67, 107, 189, 189, 189, 189, 189, 2, 2, 2, 1, 1, 1, 10, 67, 67, 107, 107] 189 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035889 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035889 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035889/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035889 Building REAL250005035890 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035890' /scratch/stefan/7916117/working/building/REAL250005035890 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005035890 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035890/0 /scratch/stefan/7916117/working/building/REAL250005035890 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/462 `/scratch/stefan/7916117/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+](CC(=O)NCCC1=NC(=O)O[N-]1)C1CCSC1) `REAL250005035890.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035890 none C[N@H+](CC(=O)NCCC1=NC(=O)O[N-]1)C1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'S.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, 9, 6, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 4, 15, 15, 15, 44, 51, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 15, 44, 44, 51, 51, 1, 1, 1, 1, 1, 1, 1] 101 rigid atoms, others: [32, 1, 34, 35, 36, 33, 15, 16, 17, 18, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035890 none C[N@H+](CC(=O)NCCC1=NC(=O)O[N-]1)C1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'S.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, 9, 6, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 73, 73, 73, 17, 8, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 101, 101, 101, 101, 99, 99, 73, 17, 17, 8, 8, 101, 101, 101, 101, 101, 101, 101] 101 rigid atoms, others: [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, 33, 34, 35, 36]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035890 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035890/1 /scratch/stefan/7916117/working/building/REAL250005035890 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/463 `/scratch/stefan/7916117/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+](CC(=O)NCCC1=NC(=O)O[N-]1)C1CCSC1) `REAL250005035890.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035890 none C[N@@H+](CC(=O)NCCC1=NC(=O)O[N-]1)C1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'S.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, 9, 6, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 5, 13, 13, 13, 32, 38, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 13, 32, 32, 38, 38, 1, 1, 1, 1, 1, 1, 1] 72 rigid atoms, others: [32, 1, 34, 35, 36, 33, 15, 16, 17, 18, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035890 none C[N@@H+](CC(=O)NCCC1=NC(=O)O[N-]1)C1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'S.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, 9, 6, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 52, 52, 52, 17, 8, 1, 1, 1, 1, 1, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 52, 17, 17, 8, 8, 72, 72, 72, 72, 72, 72, 72] 72 rigid atoms, others: [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, 33, 34, 35, 36]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035890 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `2' /scratch/stefan/7916117/working/building/REAL250005035890/2 /scratch/stefan/7916117/working/building/REAL250005035890 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 2 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/464 `/scratch/stefan/7916117/working/3D/464' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NCCC1=NC(=O)O[N-]1)C1CCSC1) `REAL250005035890.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005035890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035890/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035890 none CN(CC(=O)NCCC1=NC(=O)O[N-]1)C1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'S.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, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 12, 34, 34, 34, 100, 106, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 34, 100, 100, 106, 106, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 577 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: REAL250005035890 none CN(CC(=O)NCCC1=NC(=O)O[N-]1)C1CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'S.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, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 149, 58, 58, 58, 19, 8, 1, 1, 1, 1, 1, 1, 1, 177, 201, 201, 201, 201, 177, 177, 177, 149, 149, 58, 19, 19, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 782 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035890 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035890 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035890/0.* 2: /scratch/stefan/7916117/working/building/REAL250005035890/2.* 1: /scratch/stefan/7916117/working/building/REAL250005035890/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035890 Building REAL250005035891 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035891' /scratch/stefan/7916117/working/building/REAL250005035891 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035891 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035891/0 /scratch/stefan/7916117/working/building/REAL250005035891 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/465 `/scratch/stefan/7916117/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CCC)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035891.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035891 none CCCC(CCC)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 154, 107, 37, 107, 154, 176, 37, 37, 8, 8, 1, 1, 1, 1, 1, 1, 1, 182, 182, 182, 175, 182, 163, 163, 107, 163, 163, 176, 170, 176, 176, 176, 36, 8, 8, 8, 8] 201 rigid atoms, others: [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, 36, 37]) total number of confs: 1198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035891 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035891 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035891/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035891 Building REAL250005035892 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035892' /scratch/stefan/7916117/working/building/REAL250005035892 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035892 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035892/0 /scratch/stefan/7916117/working/building/REAL250005035892 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/466 `/scratch/stefan/7916117/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005035892.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035892 none CCN1C=C(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 133, 133, 133, 109, 60, 109, 60, 60, 17, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 201, 201, 201, 201, 201, 133, 60, 17, 17, 8, 8, 133] 201 rigid atoms, others: [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]) total number of confs: 799 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035892 none CCN1C=C(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 59, 61, 133, 133, 133, 133, 133, 1, 1, 6, 6, 6, 6, 6, 1, 21, 59, 59, 61, 61, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 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/7916117/working/building/REAL250005035892 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035892 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035892/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035892 Building REAL250005035893 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035893' /scratch/stefan/7916117/working/building/REAL250005035893 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035893 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035893/0 /scratch/stefan/7916117/working/building/REAL250005035893 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/467 `/scratch/stefan/7916117/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl) `REAL250005035893.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035893 none CC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 125, 150, 150, 95, 95, 95, 24, 8, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 150, 150, 150, 95, 24, 24, 8, 8] 150 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035893 none CC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 43, 71, 150, 150, 150, 150, 150, 1, 1, 2, 2, 2, 1, 1, 1, 7, 43, 43, 71, 71] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 22, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 427 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035893 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035893 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035893/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035893 Building REAL250005035894 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035894' /scratch/stefan/7916117/working/building/REAL250005035894 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035894 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035894/0 /scratch/stefan/7916117/working/building/REAL250005035894 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/468 `/scratch/stefan/7916117/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CC(=O)NCCC2=NC(=O)O[N-]2)CCCCC1) `REAL250005035894.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035894 none CC1(CC(=O)NCCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 92, 50, 50, 50, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 92, 92, 50, 19, 19, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 740 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035894 none CC1(CC(=O)NCCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 21, 21, 21, 79, 91, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 21, 79, 79, 91, 91, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 33, 38, 32, 34, 14, 15, 16, 17, 18, 37, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 526 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035894 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035894 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035894/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035894 Building REAL250005035895 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035895' /scratch/stefan/7916117/working/building/REAL250005035895 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035895 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035895/0 /scratch/stefan/7916117/working/building/REAL250005035895 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/469 `/scratch/stefan/7916117/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)CCCO1) `REAL250005035895.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035895 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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, 76, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 76, 24, 24, 8, 8, 111, 111, 111, 111, 111, 111] 111 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL250005035895 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 35, 56, 111, 111, 111, 111, 111, 1, 1, 1, 1, 2, 2, 2, 7, 35, 35, 56, 56, 1, 1, 1, 1, 1, 1] 111 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035895 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035895 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035895/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035895 Building REAL250005035896 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035896' /scratch/stefan/7916117/working/building/REAL250005035896 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035896 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035896/0 /scratch/stefan/7916117/working/building/REAL250005035896 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/470 `/scratch/stefan/7916117/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1CCOCC1) `REAL250005035896.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035896 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 24, 24, 24, 88, 105, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 24, 88, 88, 105, 105, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 33, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL250005035896 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 71, 71, 71, 20, 8, 1, 1, 1, 1, 1, 1, 1, 178, 201, 201, 201, 201, 201, 178, 178, 178, 178, 70, 20, 20, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 775 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035896 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035896 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035896/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035896 Building REAL250005035897 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035897' /scratch/stefan/7916117/working/building/REAL250005035897 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035897 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035897/0 /scratch/stefan/7916117/working/building/REAL250005035897 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/471 `/scratch/stefan/7916117/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC(C)(C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035897.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035897 none COC(=O)CC(C)(C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 161, 201, 115, 70, 113, 117, 33, 33, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 161, 161, 117, 117, 117, 117, 117, 117, 78, 78, 32, 9, 8, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 930 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035897 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035897 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035897/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035897 Building REAL250005035898 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035898' /scratch/stefan/7916117/working/building/REAL250005035898 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035898 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035898/0 /scratch/stefan/7916117/working/building/REAL250005035898 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/472 `/scratch/stefan/7916117/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=NN2C=C1) `REAL250005035898.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035898 none CC1=CC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=NN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 77, 77, 77, 23, 8, 1, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 201, 201, 201, 201, 76, 24, 24, 8, 8, 200, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 421 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035898 none CC1=CC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=NN2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 12, 12, 12, 61, 84, 200, 200, 200, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 61, 61, 84, 84, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 16, 17, 18, 19, 20, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 527 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035898 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035898 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035898/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035898 Building REAL250005035899 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035899' /scratch/stefan/7916117/working/building/REAL250005035899 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035899 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035899/0 /scratch/stefan/7916117/working/building/REAL250005035899 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/473 `/scratch/stefan/7916117/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005035899.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035899 none C=CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 8, 36, 36, 36, 113, 113, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 6, 6, 6, 3, 8, 8, 36, 113, 113, 113, 113, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 35, 36, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL250005035899 none C=CC(CC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 185, 138, 42, 42, 42, 15, 7, 1, 1, 1, 1, 1, 1, 1, 185, 201, 201, 201, 201, 201, 200, 200, 200, 185, 138, 138, 42, 15, 15, 7, 7, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 33, 34, 35, 36]) total number of confs: 869 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035899 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035899 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035899/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035899 Building REAL250005035900 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035900' /scratch/stefan/7916117/working/building/REAL250005035900 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035900 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035900/0 /scratch/stefan/7916117/working/building/REAL250005035900 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/474 `/scratch/stefan/7916117/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1F) `REAL250005035900.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035900 none CC1=CC=C(F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 74, 74, 74, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 73, 22, 22, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035900 none CC1=CC=C(F)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 71, 105, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 13, 71, 71, 105, 105] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035900 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035900 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035900/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035900 Building REAL250005035901 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035901' /scratch/stefan/7916117/working/building/REAL250005035901 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035901 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035901/0 /scratch/stefan/7916117/working/building/REAL250005035901 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/475 `/scratch/stefan/7916117/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C(C)(C)C)=N1) `REAL250005035901.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035901 none CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C(C)(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 5, 5, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 80, 80, 80, 24, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 151, 151, 151, 128, 128, 128, 128, 128, 80, 24, 24, 8, 8, 151, 151, 151, 151, 151, 151, 151, 151, 151] 151 rigid atoms, others: [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, 33, 34, 35, 36, 37, 38]) total number of confs: 476 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035901 none CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C(C)(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 5, 5, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 34, 54, 128, 128, 128, 128, 128, 1, 1, 4, 4, 4, 1, 2, 2, 2, 1, 6, 34, 34, 54, 54, 4, 4, 4, 4, 4, 4, 4, 4, 4] 151 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035901 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035901 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035901/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035901 Building REAL250005035902 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035902' /scratch/stefan/7916117/working/building/REAL250005035902 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035902 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035902/0 /scratch/stefan/7916117/working/building/REAL250005035902 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/476 `/scratch/stefan/7916117/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035902.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035902 none CN1CCOCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 133, 133, 133, 91, 91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 91, 24, 24, 8, 8] 133 rigid atoms, others: [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]) 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: REAL250005035902 none CN1CCOCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 43, 65, 133, 133, 133, 133, 133, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 43, 43, 65, 65] 133 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 26, 27] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035902 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035902 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035902/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035902 Building REAL250005035903 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035903' /scratch/stefan/7916117/working/building/REAL250005035903 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035903 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035903/0 /scratch/stefan/7916117/working/building/REAL250005035903 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/477 `/scratch/stefan/7916117/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005035903.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035903 none COC(=O)C1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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: [182, 176, 121, 182, 121, 121, 121, 99, 99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 122, 122, 183, 183, 183, 121, 98, 24, 24, 8, 8, 122] 183 rigid atoms, others: [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]) total number of confs: 593 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035903 none COC(=O)C1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 5, 5, 5, 27, 44, 121, 121, 121, 121, 121, 1, 1, 13, 13, 13, 1, 5, 27, 27, 44, 44, 1] 183 rigid atoms, others: [2, 4, 5, 6, 7, 8, 19, 20, 24, 30] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035903 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035903 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035903/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035903 Building REAL250005035904 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035904' /scratch/stefan/7916117/working/building/REAL250005035904 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035904 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035904/0 /scratch/stefan/7916117/working/building/REAL250005035904 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/478 `/scratch/stefan/7916117/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CCC(=O)NCCC2=NC(=O)O[N-]2)CCC(=O)N1) `REAL250005035904.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035904 none CC1(CCC(=O)NCCC2=NC(=O)O[N-]2)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 121, 121, 43, 43, 43, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 121, 121, 121, 121, 43, 17, 17, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 33, 34, 35, 36]) total number of confs: 752 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: REAL250005035904 none CC1(CCC(=O)NCCC2=NC(=O)O[N-]2)CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 31, 31, 31, 100, 101, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 31, 102, 102, 103, 103, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 34, 15, 16, 17, 18, 19] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 546 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035904 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035904 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035904/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035904 Building REAL250005035905 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035905' /scratch/stefan/7916117/working/building/REAL250005035905 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035905 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035905/0 /scratch/stefan/7916117/working/building/REAL250005035905 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/479 `/scratch/stefan/7916117/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CN2C(=O)NN=C12) `REAL250005035905.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035905 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CN2C(=O)NN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 74, 105, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 74, 74, 105, 105, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 595 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035905 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CN2C(=O)NN=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 24, 8, 1, 1, 1, 1, 1, 1, 1, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 113, 25, 25, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035905 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035905 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035905/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035905 Building REAL250005035906 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035906' /scratch/stefan/7916117/working/building/REAL250005035906 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035906 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035906/0 /scratch/stefan/7916117/working/building/REAL250005035906 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/480 `/scratch/stefan/7916117/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=CNC2=N1) `REAL250005035906.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035906 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [9, 1, 9, 9, 42, 52, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 41, 41, 52, 52, 1, 1, 1, 1] 87 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) 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: REAL250005035906 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [58, 58, 23, 8, 1, 1, 1, 1, 1, 1, 1, 58, 87, 87, 87, 87, 87, 87, 87, 87, 58, 23, 23, 8, 8, 87, 87, 87, 87] 87 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035906 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035906/1 /scratch/stefan/7916117/working/building/REAL250005035906 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/481 `/scratch/stefan/7916117/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=CN=C2N1) `REAL250005035906.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035906 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=CN=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [12, 1, 12, 12, 66, 97, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 66, 66, 97, 97, 1, 1, 1, 1] 160 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 510 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035906 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2N=CN=C2N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [80, 80, 24, 8, 1, 1, 1, 1, 1, 1, 1, 80, 160, 160, 160, 160, 160, 160, 160, 160, 79, 24, 24, 8, 8, 160, 160, 160, 160] 160 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 372 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035906 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035906 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035906/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035906/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035906 Building REAL250005035907 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035907' /scratch/stefan/7916117/working/building/REAL250005035907 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035907 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035907/0 /scratch/stefan/7916117/working/building/REAL250005035907 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/482 `/scratch/stefan/7916117/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CN=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035907.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035907 none CCC1=CC=CN=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 171, 171, 171, 171, 171, 171, 86, 86, 86, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 171, 171, 171, 85, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 580 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035907 none CCC1=CC=CN=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 43, 57, 171, 171, 171, 171, 171, 6, 6, 6, 6, 6, 1, 1, 1, 10, 43, 43, 57, 57] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/7916117/working/building/REAL250005035907 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035907 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035907/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035907 Building REAL250005035908 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035908' /scratch/stefan/7916117/working/building/REAL250005035908 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035908 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035908/0 /scratch/stefan/7916117/working/building/REAL250005035908 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/483 `/scratch/stefan/7916117/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C(F)F)=N1) `REAL250005035908.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035908 none CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [191, 191, 191, 92, 92, 92, 24, 8, 1, 1, 1, 1, 1, 1, 1, 191, 191, 201, 201, 191, 191, 191, 191, 191, 92, 24, 24, 8, 8, 201] 201 rigid atoms, others: [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]) total number of confs: 492 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035908 none CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C(F)F)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 8, 39, 62, 191, 191, 191, 191, 191, 1, 1, 10, 10, 1, 2, 2, 2, 1, 8, 39, 39, 62, 62, 10] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 19, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035908 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035908 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035908/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035908 Building REAL250005035909 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035909' /scratch/stefan/7916117/working/building/REAL250005035909 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035909 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035909/0 /scratch/stefan/7916117/working/building/REAL250005035909 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/484 `/scratch/stefan/7916117/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035909.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035909 none CC1=CC=CC=C1C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 159, 201, 201, 159, 55, 159, 159, 55, 55, 17, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 159, 201, 201, 55, 17, 17, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 771 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035909 none CC1=CC=CC=C1C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 35, 35, 35, 103, 111, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 35, 103, 103, 111, 111] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035909 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035909 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035909/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035909 Building REAL250005035910 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035910' /scratch/stefan/7916117/working/building/REAL250005035910 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035910 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035910/0 /scratch/stefan/7916117/working/building/REAL250005035910 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/485 `/scratch/stefan/7916117/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)OCC(C)(C(=O)NCCC2=NC(=O)O[N-]2)CO1) `REAL250005035910.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035910 none CC1(C)OCC(C)(C(=O)NCCC2=NC(=O)O[N-]2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', '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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 111, 201, 112, 112, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 25, 25, 8, 8, 201, 201] 201 rigid atoms, others: [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, 36, 37]) total number of confs: 635 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035910 none CC1(C)OCC(C)(C(=O)NCCC2=NC(=O)O[N-]2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', '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, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 44, 77, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 44, 44, 77, 77, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 36] set([32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035910 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035910 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035910/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035910 Building REAL250005035911 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035911' /scratch/stefan/7916117/working/building/REAL250005035911 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035911 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035911/0 /scratch/stefan/7916117/working/building/REAL250005035911 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/486 `/scratch/stefan/7916117/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005035911.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035911 none COCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 197, 150, 134, 52, 52, 52, 17, 8, 1, 1, 1, 1, 1, 1, 1, 134, 134, 201, 201, 201, 197, 197, 150, 150, 52, 17, 17, 8, 8, 134, 134, 134, 134] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 804 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: REAL250005035911 none COCCC1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [14, 6, 4, 1, 1, 1, 6, 6, 6, 30, 38, 134, 134, 134, 134, 134, 1, 1, 14, 14, 14, 6, 6, 4, 4, 6, 30, 30, 38, 38, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 16, 17, 30, 31] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 315 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035911 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035911 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035911/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035911 Building REAL250005035912 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035912' /scratch/stefan/7916117/working/building/REAL250005035912 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035912 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035912/0 /scratch/stefan/7916117/working/building/REAL250005035912 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/487 `/scratch/stefan/7916117/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1) `REAL250005035912.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035912 none CCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 200, 80, 80, 81, 55, 55, 56, 19, 8, 1, 1, 1, 1, 1, 1, 1, 80, 80, 201, 201, 201, 201, 201, 200, 200, 81, 55, 19, 19, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035912 none CCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [14, 8, 1, 1, 1, 1, 1, 6, 6, 6, 18, 25, 81, 81, 81, 80, 80, 1, 1, 14, 14, 14, 14, 14, 8, 8, 1, 6, 18, 18, 25, 25] 201 rigid atoms, others: [2, 3, 4, 5, 6, 17, 18, 26] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035912 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035912 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035912/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035912 Building REAL250005035913 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035913' /scratch/stefan/7916117/working/building/REAL250005035913 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035913 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035913/0 /scratch/stefan/7916117/working/building/REAL250005035913 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/488 `/scratch/stefan/7916117/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1CCCCC1) `REAL250005035913.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035913 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 57, 79, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 8, 8, 8, 7, 7, 7, 12, 57, 57, 79, 79, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 40, 41, 39, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 529 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: REAL250005035913 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 63, 171, 63, 63, 20, 8, 1, 1, 1, 1, 1, 1, 1, 171, 190, 201, 201, 201, 190, 171, 171, 171, 171, 171, 171, 63, 20, 20, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 915 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035913 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035913 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035913/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035913 Building REAL250005035914 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035914' /scratch/stefan/7916117/working/building/REAL250005035914 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035914 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035914/0 /scratch/stefan/7916117/working/building/REAL250005035914 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/489 `/scratch/stefan/7916117/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1OCCC2=CC=CC=C21) `REAL250005035914.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035914 none O=C(NCCC1=NC(=O)O[N-]1)C1OCCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 9, 9, 50, 70, 146, 146, 146, 146, 146, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 50, 50, 70, 70, 1, 1, 1, 1, 1, 1, 1, 1, 1] 146 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 402 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035914 none O=C(NCCC1=NC(=O)O[N-]1)C1OCCC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [79, 79, 24, 8, 1, 1, 1, 1, 1, 1, 1, 79, 146, 146, 146, 146, 146, 146, 146, 146, 146, 78, 24, 24, 8, 8, 146, 146, 146, 146, 146, 146, 146, 146, 146] 146 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035914 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035914 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035914/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035914 Building REAL250005035915 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035915' /scratch/stefan/7916117/working/building/REAL250005035915 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035915 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035915/0 /scratch/stefan/7916117/working/building/REAL250005035915 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/490 `/scratch/stefan/7916117/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035915.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035915 none CC1=CC(F)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 140, 165, 165, 165, 93, 93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 93, 24, 24, 8, 8] 165 rigid atoms, others: [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]) total number of confs: 508 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035915 none CC1=CC(F)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 62, 94, 165, 165, 165, 165, 165, 2, 2, 2, 1, 1, 1, 10, 62, 62, 94, 94] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035915 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035915 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035915/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035915 Building REAL250005035916 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035916' /scratch/stefan/7916117/working/building/REAL250005035916 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035916 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035916/0 /scratch/stefan/7916117/working/building/REAL250005035916 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/491 `/scratch/stefan/7916117/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005035916.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035916 none CC(C)OC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 136, 136, 136, 136, 136, 85, 85, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 136, 201, 201, 201, 201, 201, 201, 201, 136, 136, 136, 84, 25, 25, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035916 none CC(C)OC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [19, 6, 19, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 36, 136, 136, 136, 136, 136, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 6, 22, 22, 36, 36] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 20, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035916 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035916 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035916/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035916 Building REAL250005035917 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035917' /scratch/stefan/7916117/working/building/REAL250005035917 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035917 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035917/0 /scratch/stefan/7916117/working/building/REAL250005035917 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/492 `/scratch/stefan/7916117/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=C1C=CS2) `REAL250005035917.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035917 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=C1C=CS2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 10, 55, 80, 186, 186, 186, 186, 186, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 55, 55, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 1] 186 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 488 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: REAL250005035917 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=C1C=CS2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [96, 96, 24, 8, 1, 1, 1, 1, 1, 1, 1, 96, 186, 186, 186, 186, 186, 186, 186, 186, 95, 25, 25, 8, 8, 186, 186, 186, 186, 186, 186, 186, 186, 186] 186 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 556 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035917 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035917 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035917/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035917 Building REAL250005035918 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035918' /scratch/stefan/7916117/working/building/REAL250005035918 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035918 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035918/0 /scratch/stefan/7916117/working/building/REAL250005035918 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/493 `/scratch/stefan/7916117/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005035918.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035918 none CC(C)C1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 167, 201, 167, 167, 167, 87, 87, 87, 23, 8, 1, 1, 1, 1, 1, 1, 1, 167, 201, 201, 201, 201, 201, 201, 201, 167, 87, 23, 23, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 588 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035918 none CC(C)C1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [12, 1, 12, 1, 1, 1, 1, 1, 8, 8, 8, 46, 57, 167, 167, 167, 167, 167, 1, 13, 13, 13, 12, 13, 12, 13, 1, 9, 45, 45, 57, 57] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035918 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035918 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035918/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035918 Building REAL250005035919 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035919' /scratch/stefan/7916117/working/building/REAL250005035919 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035919 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035919/0 /scratch/stefan/7916117/working/building/REAL250005035919 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/494 `/scratch/stefan/7916117/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C(C)(C)CCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035919.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035919 none CC(=O)C(C)(C)CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 191, 201, 152, 189, 189, 152, 63, 63, 63, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 191, 189, 191, 191, 191, 189, 152, 152, 152, 152, 63, 17, 17, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 843 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035919 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035919 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035919/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035919 Building REAL250005035920 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035920' /scratch/stefan/7916117/working/building/REAL250005035920 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035920 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035920/0 /scratch/stefan/7916117/working/building/REAL250005035920 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/495 `/scratch/stefan/7916117/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(OCC(=O)NCCC2=NC(=O)O[N-]2)CCC1) `REAL250005035920.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035920 none CC1(OCC(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 132, 102, 56, 56, 56, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 102, 102, 56, 19, 19, 8, 8, 201, 201, 197, 201, 201, 201] 201 rigid atoms, others: [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, 33]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035920 none CC1(OCC(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 5, 13, 43, 43, 43, 117, 121, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 13, 13, 43, 117, 117, 121, 121, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 33, 32, 15, 16, 17, 28, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035920 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035920 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035920/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035920 Building REAL250005035921 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035921' /scratch/stefan/7916117/working/building/REAL250005035921 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035921 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035921/0 /scratch/stefan/7916117/working/building/REAL250005035921 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/496 `/scratch/stefan/7916117/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C) `REAL250005035921.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035921 none CCCCN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 79, 79, 79, 79, 41, 41, 41, 15, 7, 1, 1, 1, 1, 1, 1, 1, 79, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 41, 15, 15, 7, 7, 79, 79, 79] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 737 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035921 none CCCCN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 27, 27, 79, 79, 79, 79, 79, 1, 1, 10, 10, 10, 9, 9, 9, 9, 5, 5, 1, 6, 27, 27, 27, 27, 2, 2, 2] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 19, 20, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035921 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035921 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035921/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035921 Building REAL250005035922 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035922' /scratch/stefan/7916117/working/building/REAL250005035922 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035922 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035922/0 /scratch/stefan/7916117/working/building/REAL250005035922 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/497 `/scratch/stefan/7916117/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2C=C1) `REAL250005035922.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035922 none CC1=NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 53, 53, 53, 23, 8, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 106, 106, 106, 106, 52, 23, 23, 8, 8, 106, 106, 106] 106 rigid atoms, others: [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]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035922 none CC1=NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 60, 106, 106, 106, 106, 106, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 39, 39, 60, 60, 1, 1, 1] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 34, 33, 18, 19, 20, 21, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 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/7916117/working/building/REAL250005035922 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035922 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035922/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035922 Building REAL250005035923 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035923' /scratch/stefan/7916117/working/building/REAL250005035923 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035923 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035923/0 /scratch/stefan/7916117/working/building/REAL250005035923 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/498 `/scratch/stefan/7916117/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CCCC(=O)NCCC2=NC(=O)O[N-]2)SC=C1) `REAL250005035923.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035923 none CC1=C(CCCC(=O)NCCC2=NC(=O)O[N-]2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 130, 106, 90, 33, 33, 33, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 129, 129, 128, 128, 90, 90, 33, 17, 17, 8, 8, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 817 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: REAL250005035923 none CC1=C(CCCC(=O)NCCC2=NC(=O)O[N-]2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 6, 6, 11, 43, 43, 43, 104, 104, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 11, 11, 43, 104, 104, 104, 104, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 35, 34, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 599 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035923 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035923 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035923/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035923 Building REAL250005035924 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035924' /scratch/stefan/7916117/working/building/REAL250005035924 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035924 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035924/0 /scratch/stefan/7916117/working/building/REAL250005035924 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/499 `/scratch/stefan/7916117/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005035924.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035924 none NC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 101, 105, 101, 101, 101, 65, 65, 65, 24, 8, 1, 1, 1, 1, 1, 1, 1, 101, 105, 105, 101, 101, 64, 25, 25, 8, 8] 105 rigid atoms, others: [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]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035924 none NC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 10, 10, 10, 44, 56, 101, 101, 101, 101, 101, 1, 3, 3, 1, 1, 10, 44, 44, 56, 56] 105 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 21, 22] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 23, 24, 25, 26, 27]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035924 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035924 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035924/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035924 Building REAL250005035925 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035925' /scratch/stefan/7916117/working/building/REAL250005035925 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035925 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035925/0 /scratch/stefan/7916117/working/building/REAL250005035925 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/500 `/scratch/stefan/7916117/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005035925.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035925 none CCC(=O)N1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 171, 133, 171, 133, 133, 133, 48, 48, 48, 16, 8, 1, 1, 1, 1, 1, 1, 1, 133, 201, 201, 201, 201, 201, 133, 133, 133, 133, 133, 48, 16, 16, 8, 8, 133, 133] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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: REAL250005035925 none CCC(=O)N1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 9, 42, 44, 133, 133, 133, 133, 133, 1, 10, 10, 10, 9, 9, 1, 1, 1, 1, 1, 9, 42, 42, 44, 44, 1, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 19, 25, 26, 27, 28, 29, 36] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 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/7916117/working/building/REAL250005035925 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035925 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035925/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035925 Building REAL250005035926 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035926' /scratch/stefan/7916117/working/building/REAL250005035926 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035926 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035926/0 /scratch/stefan/7916117/working/building/REAL250005035926 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/501 `/scratch/stefan/7916117/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(Cl)=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035926.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035926 none CC1=NC(Cl)=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 16, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 143, 41, 41, 41, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 143, 143, 41, 17, 17, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 638 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035926 none CC1=NC(Cl)=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 16, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 29, 29, 29, 99, 99, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 6, 6, 29, 99, 99, 99, 99] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 541 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035926 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035926 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035926/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035926 Building REAL250005035927 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035927' /scratch/stefan/7916117/working/building/REAL250005035927 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035927 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035927/0 /scratch/stefan/7916117/working/building/REAL250005035927 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/502 `/scratch/stefan/7916117/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@@H+]1C1CCCC1) `REAL250005035927.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035927 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 13, 16, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 13, 13, 16, 16, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 40 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 103 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: REAL250005035927 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 15, 9, 1, 1, 1, 1, 1, 1, 1, 31, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 31, 15, 15, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 40 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035927 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 3, 3, 13, 16, 40, 40, 40, 40, 40, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 3, 13, 13, 16, 16, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 40 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 101 number of broken/clashed sets: 25 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035927 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035927/1 /scratch/stefan/7916117/working/building/REAL250005035927 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/503 `/scratch/stefan/7916117/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@H+]1C1CCCC1) `REAL250005035927.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035927 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 16, 20, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 16, 16, 20, 20, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 46 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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: REAL250005035927 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 35, 14, 8, 1, 1, 1, 1, 1, 1, 1, 35, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 35, 14, 14, 8, 8, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46] 46 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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: REAL250005035927 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@H+]1C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 6, 6, 17, 21, 46, 46, 46, 46, 46, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 17, 17, 21, 21, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 46 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 126 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035927 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035927 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035927/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035927/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035927 Building REAL250005035928 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035928' /scratch/stefan/7916117/working/building/REAL250005035928 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035928 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035928/0 /scratch/stefan/7916117/working/building/REAL250005035928 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/504 `/scratch/stefan/7916117/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1) `REAL250005035928.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035928 none N#CC1=CC=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 7, 1, 1, 1, 11, 11, 11, 49, 51, 139, 139, 139, 139, 139, 1, 1, 7, 7, 7, 7, 11, 49, 49, 51, 51, 1, 1, 1, 1, 7] 201 rigid atoms, others: [32, 33, 6, 7, 8, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 314 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035928 none N#CC1=CC=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 1, 7, 33, 33, 33, 101, 102, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 33, 101, 101, 102, 102, 7, 7, 7, 7, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 21, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 536 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: REAL250005035928 none N#CC1=CC=CC(C2(C(=O)NCCC3=NC(=O)O[N-]3)CC2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 139, 45, 45, 45, 17, 8, 1, 1, 1, 1, 1, 1, 1, 139, 139, 201, 201, 201, 201, 45, 17, 17, 8, 8, 139, 139, 139, 139, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 532 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035928 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035928 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035928/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035928 Building REAL250005035929 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035929' /scratch/stefan/7916117/working/building/REAL250005035929 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035929 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035929/0 /scratch/stefan/7916117/working/building/REAL250005035929 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/505 `/scratch/stefan/7916117/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005035929.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035929 none CC(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.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, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 167, 201, 167, 167, 167, 80, 80, 80, 24, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 201, 201, 201, 201, 201, 201, 201, 167, 167, 79, 24, 24, 8, 8, 167] 201 rigid atoms, others: [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]) total number of confs: 588 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035929 none CC(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.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, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [5, 1, 5, 1, 1, 1, 1, 1, 5, 5, 5, 31, 58, 167, 167, 167, 167, 167, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 31, 31, 58, 58, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 18, 19, 27, 28] set([0, 2, 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: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035929 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035929 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035929/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035929 Building REAL250005035930 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035930' /scratch/stefan/7916117/working/building/REAL250005035930 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035930 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035930/0 /scratch/stefan/7916117/working/building/REAL250005035930 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/506 `/scratch/stefan/7916117/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C2CC2C(=O)NCCC2=NC(=O)O[N-]2)SC=C1) `REAL250005035930.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035930 none CC1=C(C2CC2C(=O)NCCC2=NC(=O)O[N-]2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [4, 4, 1, 1, 1, 1, 1, 8, 8, 8, 39, 53, 147, 147, 147, 147, 147, 4, 4, 4, 5, 5, 5, 1, 1, 1, 1, 8, 39, 39, 53, 53, 4, 4] 162 rigid atoms, others: [2, 3, 4, 5, 6, 23, 24, 25, 26] set([0, 1, 7, 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: 354 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035930 none CC1=C(C2CC2C(=O)NCCC2=NC(=O)O[N-]2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 63, 73, 162, 162, 162, 162, 162, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 14, 63, 63, 73, 73, 1, 1] 162 rigid atoms, others: [0, 1, 2, 3, 33, 32, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035930 none CC1=C(C2CC2C(=O)NCCC2=NC(=O)O[N-]2)SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 147, 147, 147, 73, 73, 73, 24, 8, 1, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 162, 147, 147, 147, 147, 72, 24, 24, 8, 8, 162, 162] 162 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 506 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035930 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035930 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035930/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035930 Building REAL250005035931 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035931' /scratch/stefan/7916117/working/building/REAL250005035931 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035931 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035931/0 /scratch/stefan/7916117/working/building/REAL250005035931 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/507 `/scratch/stefan/7916117/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1(O)CCCCC1)NCCC1=NC(=O)O[N-]1) `REAL250005035931.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035931 none O=C(CC1(O)CCCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 160, 201, 201, 201, 201, 201, 198, 20, 8, 1, 1, 1, 1, 1, 1, 1, 160, 160, 603, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 20, 20, 8, 8] 603 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1400 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: REAL250005035931 none O=C(CC1(O)CCCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 85, 101, 201, 201, 201, 200, 201, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 85, 85, 101, 101] 603 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 35, 36, 33, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21]) total number of confs: 572 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035931 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035931 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035931/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035931 Building REAL250005035932 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035932' /scratch/stefan/7916117/working/building/REAL250005035932 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035932 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035932/0 /scratch/stefan/7916117/working/building/REAL250005035932 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/508 `/scratch/stefan/7916117/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)N1C=CC=C1) `REAL250005035932.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035932 none CC(C(=O)NCCC1=NC(=O)O[N-]1)N1C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 9, 31, 31, 31, 105, 114, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 9, 9, 9, 9, 31, 105, 105, 114, 114, 1, 1, 1, 1] 201 rigid atoms, others: [1, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 590 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035932 none CC(C(=O)NCCC1=NC(=O)O[N-]1)N1C=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [198, 74, 74, 74, 22, 8, 1, 1, 1, 1, 1, 1, 1, 198, 201, 201, 201, 201, 198, 198, 198, 198, 74, 23, 22, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035932 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035932 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035932/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035932 Building REAL250005035933 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035933' /scratch/stefan/7916117/working/building/REAL250005035933 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035933 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035933/0 /scratch/stefan/7916117/working/building/REAL250005035933 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/509 `/scratch/stefan/7916117/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCN2C=NC=C2C1) `REAL250005035933.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035933 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN2C=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 64, 100, 161, 161, 161, 161, 161, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 64, 64, 100, 100, 1, 1, 1, 1, 1, 1, 1, 1, 1] 161 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 534 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: REAL250005035933 none O=C(NCCC1=NC(=O)O[N-]1)C1CCN2C=NC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 8, 1, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 89, 161, 161, 161, 161, 161, 161, 161, 161, 89, 24, 24, 8, 8, 161, 161, 161, 161, 161, 161, 161, 161, 161] 161 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 515 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035933 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035933 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035933/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035933 Building REAL250005035934 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035934' /scratch/stefan/7916117/working/building/REAL250005035934 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005035934 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035934/0 /scratch/stefan/7916117/working/building/REAL250005035934 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/510 `/scratch/stefan/7916117/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](CC(=O)NCCC1=NC(=O)O[N-]1)C1CC1) `REAL250005035934.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035934 none CC[N@H+](CC(=O)NCCC1=NC(=O)O[N-]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 9, 6, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 8, 24, 24, 24, 60, 64, 118, 118, 118, 118, 118, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 24, 60, 60, 64, 64, 1, 1, 1, 1, 1] 118 rigid atoms, others: [32, 33, 2, 35, 34, 16, 17, 18, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035934 none CC[N@H+](CC(=O)NCCC1=NC(=O)O[N-]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 9, 6, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 113, 118, 72, 72, 72, 17, 8, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 118, 118, 118, 118, 113, 113, 72, 17, 17, 8, 8, 118, 118, 118, 118, 118] 118 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 461 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035934 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035934/1 /scratch/stefan/7916117/working/building/REAL250005035934 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/511 `/scratch/stefan/7916117/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](CC(=O)NCCC1=NC(=O)O[N-]1)C1CC1) `REAL250005035934.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035934 none CC[N@@H+](CC(=O)NCCC1=NC(=O)O[N-]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 9, 6, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 3, 1, 3, 3, 7, 19, 19, 19, 56, 64, 127, 127, 127, 127, 127, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 19, 56, 56, 64, 64, 1, 1, 1, 1, 1] 128 rigid atoms, others: [32, 33, 2, 35, 34, 16, 17, 18, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 358 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: REAL250005035934 none CC[N@@H+](CC(=O)NCCC1=NC(=O)O[N-]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 9, 6, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 127, 121, 127, 73, 73, 73, 17, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 128, 128, 128, 128, 128, 121, 121, 73, 17, 17, 8, 8, 127, 127, 127, 127, 127] 128 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 502 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035934 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `2' /scratch/stefan/7916117/working/building/REAL250005035934/2 /scratch/stefan/7916117/working/building/REAL250005035934 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 2 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/512 `/scratch/stefan/7916117/working/3D/512' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(=O)NCCC1=NC(=O)O[N-]1)C1CC1) `REAL250005035934.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005035934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035934/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035934 none CCN(CC(=O)NCCC1=NC(=O)O[N-]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 10, 24, 24, 24, 66, 82, 186, 186, 186, 186, 186, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 24, 66, 66, 82, 82, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 507 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: REAL250005035934 none CCN(CC(=O)NCCC1=NC(=O)O[N-]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 173, 74, 74, 74, 22, 8, 1, 1, 1, 1, 1, 1, 1, 186, 186, 186, 201, 201, 201, 201, 201, 173, 173, 74, 22, 23, 8, 8, 186, 186, 186, 186, 186] 201 rigid atoms, others: [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, 33, 34]) total number of confs: 808 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035934 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035934 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035934/0.* 2: /scratch/stefan/7916117/working/building/REAL250005035934/2.* 1: /scratch/stefan/7916117/working/building/REAL250005035934/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035934 Building REAL250005035935 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035935' /scratch/stefan/7916117/working/building/REAL250005035935 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035935 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035935/0 /scratch/stefan/7916117/working/building/REAL250005035935 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/513 `/scratch/stefan/7916117/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(C(F)F)C=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035935.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035935 none O=C(CC1=CC=C(C(F)F)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 15, 15, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [69, 69, 69, 104, 151, 151, 104, 104, 195, 195, 151, 151, 17, 8, 1, 1, 1, 1, 1, 1, 1, 104, 104, 151, 151, 195, 151, 151, 69, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 1122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035935 none O=C(CC1=CC=C(C(F)F)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 15, 15, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 29, 33, 151, 151, 151, 151, 151, 4, 4, 1, 1, 11, 1, 1, 7, 29, 29, 33, 33] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 10, 11, 23, 24, 26, 27] set([0, 1, 32, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 28, 29, 30, 31]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035935 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035935 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035935/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035935 Building REAL250005035936 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035936' /scratch/stefan/7916117/working/building/REAL250005035936 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035936 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035936/0 /scratch/stefan/7916117/working/building/REAL250005035936 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/514 `/scratch/stefan/7916117/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005035936.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035936 none CC1(C)CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 155, 52, 52, 52, 17, 8, 1, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 155, 52, 17, 17, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [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, 36, 37, 38, 39, 40, 41]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035936 none CC1(C)CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 27, 27, 27, 98, 101, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 98, 98, 101, 101, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 41, 40, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 31]) total number of confs: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035936 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035936 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035936/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035936 Building REAL250005035937 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035937' /scratch/stefan/7916117/working/building/REAL250005035937 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035937 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035937/0 /scratch/stefan/7916117/working/building/REAL250005035937 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/515 `/scratch/stefan/7916117/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035937.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035937 none CC(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 153, 201, 153, 153, 153, 153, 53, 53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 153, 201, 201, 201, 153, 153, 153, 53, 17, 17, 8, 8, 153] 201 rigid atoms, others: [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]) total number of confs: 504 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035937 none CC(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 33, 153, 153, 153, 153, 153, 1, 11, 11, 11, 1, 1, 1, 5, 29, 29, 33, 33, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 23, 24, 25, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035937 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035937 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035937/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035937 Building REAL250005035938 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035938' /scratch/stefan/7916117/working/building/REAL250005035938 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035938 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035938/0 /scratch/stefan/7916117/working/building/REAL250005035938 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/516 `/scratch/stefan/7916117/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CSC2=NC=CN12)NCCC1=NC(=O)O[N-]1) `REAL250005035938.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035938 none O=C(CC1=CSC2=NC=CN12)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [41, 41, 41, 121, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 121, 121, 201, 201, 201, 41, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035938 none O=C(CC1=CSC2=NC=CN12)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 84, 86, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 25, 84, 84, 86, 86] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035938 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035938 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035938/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035938 Building REAL250005035939 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035939' /scratch/stefan/7916117/working/building/REAL250005035939 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035939 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035939/0 /scratch/stefan/7916117/working/building/REAL250005035939 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/517 `/scratch/stefan/7916117/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035939.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035939 none CC1=CC(Cl)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 134, 165, 165, 165, 91, 91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 91, 24, 25, 8, 8] 165 rigid atoms, others: [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]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035939 none CC1=CC(Cl)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 62, 96, 165, 165, 165, 165, 165, 2, 2, 2, 1, 1, 1, 10, 62, 62, 96, 96] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035939 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035939 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035939/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035939 Building REAL250005035940 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035940' /scratch/stefan/7916117/working/building/REAL250005035940 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035940 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035940/0 /scratch/stefan/7916117/working/building/REAL250005035940 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/518 `/scratch/stefan/7916117/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCN1C=CC=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035940.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035940 none O=C(CCCN1C=CC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 145, 131, 199, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 145, 145, 180, 180, 190, 190, 201, 201, 201, 201, 39, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 1116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035940 none O=C(CCCN1C=CC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 15, 9, 6, 1, 1, 1, 1, 1, 1, 33, 33, 102, 102, 201, 201, 201, 201, 201, 14, 14, 9, 9, 6, 6, 1, 1, 1, 1, 32, 102, 102, 102, 102] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035940 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035940 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035940/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035940 Building REAL250005035941 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035941' /scratch/stefan/7916117/working/building/REAL250005035941 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035941 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035941/0 /scratch/stefan/7916117/working/building/REAL250005035941 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/519 `/scratch/stefan/7916117/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1COC(=O)C1)NCCC1=NC(=O)O[N-]1) `REAL250005035941.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035941 none O=C(CC1COC(=O)C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 11, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 5, 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: [67, 67, 67, 191, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 191, 191, 201, 201, 201, 201, 201, 67, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 763 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035941 none O=C(CC1COC(=O)C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 11, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 5, 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: [30, 6, 1, 1, 1, 1, 1, 1, 1, 30, 30, 109, 116, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 30, 109, 109, 116, 116] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035941 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035941 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035941/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035941 Building REAL250005035942 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035942' /scratch/stefan/7916117/working/building/REAL250005035942 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035942 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035942/0 /scratch/stefan/7916117/working/building/REAL250005035942 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/520 `/scratch/stefan/7916117/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)NCCC1=NC(=O)O[N-]1)[NH+](C)C) `REAL250005035942.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035942 none CCCC(C(=O)NCCC1=NC(=O)O[N-]1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 168, 133, 54, 54, 54, 8, 8, 1, 1, 1, 1, 1, 1, 1, 134, 153, 153, 153, 183, 183, 183, 172, 183, 179, 179, 134, 53, 8, 8, 8, 8, 153, 153, 153, 153, 153, 153] 183 rigid atoms, others: [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, 33, 34, 35, 36, 37]) total number of confs: 923 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035942 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035942 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035942/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035942 Building REAL250005035943 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035943' /scratch/stefan/7916117/working/building/REAL250005035943 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035943 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035943/0 /scratch/stefan/7916117/working/building/REAL250005035943 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/521 `/scratch/stefan/7916117/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005035943.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035943 none CC(CCC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 9, 38, 38, 38, 113, 113, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 9, 9, 38, 113, 113, 113, 113, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL250005035943 none CC(CCC(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 109, 93, 26, 26, 26, 13, 8, 1, 1, 1, 1, 1, 1, 1, 166, 201, 201, 201, 201, 201, 166, 166, 166, 166, 121, 121, 93, 93, 26, 13, 13, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 33, 34, 35, 36, 37, 38]) total number of confs: 886 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035943 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035943 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035943/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035943 Building REAL250005035944 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035944' /scratch/stefan/7916117/working/building/REAL250005035944 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035944 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035944/0 /scratch/stefan/7916117/working/building/REAL250005035944 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/522 `/scratch/stefan/7916117/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(OCC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035944.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035944 none CC1=CC=C(F)C(OCC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 141, 62, 27, 27, 27, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 68, 68, 26, 8, 8, 8, 8, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 467 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035944 none CC1=CC=C(F)C(OCC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 11, 33, 66, 66, 66, 124, 124, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 33, 33, 66, 124, 124, 124, 124, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 24, 25, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 646 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035944 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035944 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035944/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035944 Building REAL250005035945 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035945' /scratch/stefan/7916117/working/building/REAL250005035945 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035945 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035945/0 /scratch/stefan/7916117/working/building/REAL250005035945 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/523 `/scratch/stefan/7916117/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL250005035945.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035945 none CN(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 198, 201, 198, 198, 198, 80, 80, 80, 24, 8, 1, 1, 1, 1, 1, 1, 1, 198, 198, 198, 201, 201, 201, 201, 201, 201, 198, 198, 80, 24, 24, 8, 8, 198] 201 rigid atoms, others: [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]) total number of confs: 441 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035945 none CN(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 12, 12, 12, 61, 79, 198, 198, 198, 198, 198, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 12, 61, 61, 79, 79, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 18, 19, 20, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 486 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035945 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035945 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035945/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035945 Building REAL250005035946 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035946' /scratch/stefan/7916117/working/building/REAL250005035946 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035946 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035946/0 /scratch/stefan/7916117/working/building/REAL250005035946 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/524 `/scratch/stefan/7916117/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)NCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035946.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035946 none CCOC(=O)NCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 162, 162, 139, 162, 135, 49, 81, 23, 23, 23, 11, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 139, 110, 110, 81, 81, 81, 81, 23, 11, 11, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 981 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035946 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035946 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035946/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035946 Building REAL250005035947 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035947' /scratch/stefan/7916117/working/building/REAL250005035947 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035947 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035947/0 /scratch/stefan/7916117/working/building/REAL250005035947 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/525 `/scratch/stefan/7916117/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCCCC1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035947.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035947 none CC1(C)CCCCC1CC(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in 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, 195, 86, 86, 86, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 85, 23, 23, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 774 number of broken/clashed sets: 121 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035947 none CC1(C)CCCCC1CC(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 19, 19, 19, 66, 94, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 19, 66, 66, 94, 94] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([35, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 41]) total number of confs: 572 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035947 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035947 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035947/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035947 Building REAL250005035948 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035948' /scratch/stefan/7916117/working/building/REAL250005035948 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035948 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035948/0 /scratch/stefan/7916117/working/building/REAL250005035948 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/526 `/scratch/stefan/7916117/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CSCCS1)NCCC1=NC(=O)O[N-]1) `REAL250005035948.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035948 none O=C(CC1CSCCS1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 5, 5, 14, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [68, 68, 68, 175, 201, 201, 201, 201, 201, 20, 8, 1, 1, 1, 1, 1, 1, 1, 175, 175, 201, 201, 201, 201, 201, 201, 201, 67, 20, 20, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 788 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035948 none O=C(CC1CSCCS1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 14, 5, 5, 14, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 8, 1, 1, 1, 1, 1, 1, 1, 28, 28, 96, 108, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 28, 96, 96, 108, 108] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31]) total number of confs: 580 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035948 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035948 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035948/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035948 Building REAL250005035949 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035949' /scratch/stefan/7916117/working/building/REAL250005035949 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035949 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035949/0 /scratch/stefan/7916117/working/building/REAL250005035949 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/527 `/scratch/stefan/7916117/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=CO2)N1) `REAL250005035949.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035949 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=CO2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 12, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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: [10, 1, 10, 10, 51, 67, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 1, 1, 1, 10, 50, 50, 67, 67, 1, 1, 1, 1] 110 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035949 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=CO2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 12, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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: [57, 57, 22, 8, 1, 1, 1, 1, 1, 1, 1, 57, 110, 110, 110, 110, 110, 110, 110, 57, 23, 23, 8, 8, 110, 110, 110, 110] 110 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035949 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035949 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035949/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035949 Building REAL250005035950 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035950' /scratch/stefan/7916117/working/building/REAL250005035950 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035950 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035950/0 /scratch/stefan/7916117/working/building/REAL250005035950 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/528 `/scratch/stefan/7916117/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CN=CN2C=C1) `REAL250005035950.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035950 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CN=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 42, 67, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 42, 42, 67, 67, 1, 1, 1, 1, 1] 125 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) 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: REAL250005035950 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CN=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 21, 8, 1, 1, 1, 1, 1, 1, 1, 64, 125, 125, 125, 125, 125, 125, 125, 125, 64, 21, 21, 8, 8, 125, 125, 125, 125, 125] 125 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035950 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035950/1 /scratch/stefan/7916117/working/building/REAL250005035950 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/529 `/scratch/stefan/7916117/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C[NH+]=CN2C=C1) `REAL250005035950.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035950 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C[NH+]=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 6, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 41, 57, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 57, 57, 1, 1, 1, 1, 1] 93 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035950 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C[NH+]=CN2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 6, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 17, 8, 1, 1, 1, 1, 1, 1, 1, 55, 93, 93, 93, 93, 93, 93, 93, 93, 93, 55, 17, 17, 8, 8, 93, 93, 93, 93, 93] 93 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035950 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035950 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035950/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035950/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035950 Building REAL250005035951 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035951' /scratch/stefan/7916117/working/building/REAL250005035951 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035951 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035951/0 /scratch/stefan/7916117/working/building/REAL250005035951 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/530 `/scratch/stefan/7916117/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2CCCCN2N=C1) `REAL250005035951.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035951 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2CCCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 1, 12, 12, 62, 84, 181, 181, 181, 182, 182, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 61, 61, 84, 84, 1, 1, 1, 1, 1, 1, 1, 1, 1] 182 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 485 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: REAL250005035951 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2CCCCN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 5, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [85, 85, 23, 8, 1, 1, 1, 1, 1, 1, 1, 85, 182, 182, 182, 182, 182, 182, 181, 181, 84, 23, 23, 8, 8, 182, 182, 182, 182, 182, 182, 182, 182, 181] 182 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 416 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035951 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035951 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035951/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035951 Building REAL250005035952 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035952' /scratch/stefan/7916117/working/building/REAL250005035952 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035952 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035952/0 /scratch/stefan/7916117/working/building/REAL250005035952 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/531 `/scratch/stefan/7916117/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(Cl)C=N1) `REAL250005035952.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035952 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(Cl)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 3, 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: [11, 1, 11, 11, 47, 54, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1, 1, 11, 47, 47, 54, 54, 1, 1] 96 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) 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: REAL250005035952 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C(Cl)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 16, 1, 8, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 3, 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: [64, 64, 20, 8, 1, 1, 1, 1, 1, 1, 1, 64, 96, 96, 96, 96, 96, 96, 64, 20, 20, 8, 8, 96, 96] 96 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035952 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035952 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035952/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035952 Building REAL250005035953 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035953' /scratch/stefan/7916117/working/building/REAL250005035953 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035953 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035953/0 /scratch/stefan/7916117/working/building/REAL250005035953 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/532 `/scratch/stefan/7916117/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(N)=N1) `REAL250005035953.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035953 none CC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(N)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.pl3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 134, 174, 174, 97, 97, 97, 20, 8, 1, 1, 1, 1, 1, 1, 1, 174, 174, 174, 174, 174, 174, 174, 97, 20, 20, 8, 8, 174, 174] 174 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 580 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: REAL250005035953 none CC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(N)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.pl3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 65, 102, 174, 174, 174, 174, 174, 1, 1, 1, 2, 2, 2, 1, 12, 65, 65, 102, 102, 2, 2] 174 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 560 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035953 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035953 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035953/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035953 Building REAL250005035954 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035954' /scratch/stefan/7916117/working/building/REAL250005035954 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035954 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035954/0 /scratch/stefan/7916117/working/building/REAL250005035954 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/533 `/scratch/stefan/7916117/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(Cl)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035954.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035954 none CC1=NC(Cl)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 171, 171, 171, 171, 97, 97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 171, 97, 24, 24, 8, 8] 171 rigid atoms, others: [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]) 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: REAL250005035954 none CC1=NC(Cl)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 16, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 64, 96, 171, 171, 171, 171, 171, 2, 2, 2, 1, 1, 10, 64, 64, 96, 96] 171 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035954 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035954 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035954/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035954 Building REAL250005035955 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035955' /scratch/stefan/7916117/working/building/REAL250005035955 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035955 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035955/0 /scratch/stefan/7916117/working/building/REAL250005035955 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/534 `/scratch/stefan/7916117/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)S1) `REAL250005035955.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035955 none CC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 96, 96, 96, 24, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 96, 25, 25, 8, 8, 165, 165, 165] 165 rigid atoms, others: [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]) total number of confs: 407 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035955 none CC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 51, 71, 165, 165, 165, 165, 165, 1, 1, 1, 2, 2, 2, 9, 50, 50, 72, 72, 2, 2, 2] 165 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035955 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035955 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035955/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035955 Building REAL250005035956 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035956' /scratch/stefan/7916117/working/building/REAL250005035956 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035956 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035956/0 /scratch/stefan/7916117/working/building/REAL250005035956 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/535 `/scratch/stefan/7916117/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005035956.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035956 none CC1=CC(Cl)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 150, 150, 91, 91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 150, 150, 91, 25, 25, 8, 8, 150] 150 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 368 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035956 none CC1=CC(Cl)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 47, 76, 150, 150, 150, 150, 150, 1, 1, 2, 2, 2, 1, 7, 47, 47, 76, 76, 1] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 22, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035956 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035956 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035956/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035956 Building REAL250005035957 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035957' /scratch/stefan/7916117/working/building/REAL250005035957 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035957 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035957/0 /scratch/stefan/7916117/working/building/REAL250005035957 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/536 `/scratch/stefan/7916117/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1[O-]) `REAL250005035957.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035957 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 14, 14, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 14, 14, 14, 1, 1, 1] 23 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005035957 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 7, 7, 1, 1, 1, 1, 1, 1, 1, 17, 23, 23, 17, 23, 23, 23, 23, 17, 8, 8, 7, 7, 23, 23, 23] 23 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035957 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035957/1 /scratch/stefan/7916117/working/building/REAL250005035957 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/537 `/scratch/stefan/7916117/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1O) `REAL250005035957.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035957 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 246 conformations in input total number of sets (complete confs): 246 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 47, 62, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 1, 1, 10, 47, 47, 62, 62, 1, 1, 1, 2] 246 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 27]) total number of confs: 351 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: REAL250005035957 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 246 conformations in input total number of sets (complete confs): 246 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 21, 8, 1, 1, 1, 1, 1, 1, 1, 69, 123, 123, 116, 123, 123, 123, 123, 69, 21, 21, 8, 8, 123, 123, 123, 246] 246 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 594 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035957 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035957 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035957/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035957/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035957 Building REAL250005035958 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035958' /scratch/stefan/7916117/working/building/REAL250005035958 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035958 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035958/0 /scratch/stefan/7916117/working/building/REAL250005035958 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/538 `/scratch/stefan/7916117/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=N1) `REAL250005035958.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035958 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 191, 191, 91, 91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 190, 190, 191, 201, 201, 201, 201, 201, 90, 25, 25, 8, 8, 190] 201 rigid atoms, others: [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]) 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: REAL250005035958 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 1, 1, 1, 1, 9, 9, 9, 48, 61, 190, 190, 190, 191, 191, 1, 1, 1, 5, 5, 5, 5, 5, 9, 47, 47, 62, 62, 1] 201 rigid atoms, others: [1, 2, 3, 4, 15, 16, 17, 28] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035958 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035958 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035958/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035958 Building REAL250005035959 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035959' /scratch/stefan/7916117/working/building/REAL250005035959 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035959 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035959/0 /scratch/stefan/7916117/working/building/REAL250005035959 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/539 `/scratch/stefan/7916117/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=C(F)C=C1F)NCCC1=NC(=O)O[N-]1) `REAL250005035959.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035959 none O=C(CCC1=CC=C(F)C=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [47, 47, 47, 143, 170, 201, 201, 195, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 170, 170, 201, 201, 201, 47, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 809 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035959 none O=C(CCC1=CC=C(F)C=C1F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [31, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 100, 103, 201, 201, 201, 201, 201, 9, 9, 5, 5, 1, 1, 1, 31, 101, 101, 103, 103] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27] set([0, 1, 2, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 568 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035959 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035959 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035959/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035959 Building REAL250005035960 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035960' /scratch/stefan/7916117/working/building/REAL250005035960 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035960 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035960/0 /scratch/stefan/7916117/working/building/REAL250005035960 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/540 `/scratch/stefan/7916117/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2CCCCC2=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035960.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035960 none CN1N=C2CCCCC2=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 167, 167, 167, 167, 167, 83, 83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 83, 24, 24, 8, 8] 167 rigid atoms, others: [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]) total number of confs: 389 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: REAL250005035960 none CN1N=C2CCCCC2=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 59, 81, 167, 167, 167, 167, 167, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 59, 59, 81, 81] 167 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 470 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035960 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035960 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035960/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035960 Building REAL250005035961 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035961' /scratch/stefan/7916117/working/building/REAL250005035961 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035961 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035961/0 /scratch/stefan/7916117/working/building/REAL250005035961 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/541 `/scratch/stefan/7916117/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1CC(C(=O)NCCC2=NC(=O)O[N-]2)CCO1) `REAL250005035961.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035961 none CCCC1CC(C(=O)NCCC2=NC(=O)O[N-]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 131, 131, 131, 47, 47, 47, 19, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 201, 201, 201, 201, 201, 193, 193, 131, 131, 131, 131, 47, 19, 19, 8, 8, 131, 131, 131, 131] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 756 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035961 none CCCC1CC(C(=O)NCCC2=NC(=O)O[N-]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 1, 1, 1, 1, 1, 12, 12, 12, 51, 55, 131, 131, 131, 131, 131, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 1, 1, 1, 1, 12, 51, 51, 55, 55, 1, 1, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 39, 38, 17, 18, 19, 36, 27, 28, 29, 30, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035961 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035961 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035961/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035961 Building REAL250005035962 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035962' /scratch/stefan/7916117/working/building/REAL250005035962 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035962 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035962/0 /scratch/stefan/7916117/working/building/REAL250005035962 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/542 `/scratch/stefan/7916117/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1=CSC=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035962.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035962 none O=C(CCCC1=CSC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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, 25, 25, 81, 85, 113, 201, 201, 201, 201, 11, 6, 1, 1, 1, 1, 1, 1, 1, 81, 81, 113, 113, 113, 113, 201, 201, 201, 25, 11, 11, 6, 6] 201 rigid atoms, others: [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]) total number of confs: 828 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035962 none O=C(CCCC1=CSC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 14, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [34, 6, 2, 2, 1, 1, 1, 1, 1, 1, 34, 34, 103, 103, 201, 201, 201, 201, 201, 6, 6, 2, 2, 2, 2, 1, 1, 1, 34, 103, 103, 103, 103] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32]) total number of confs: 594 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035962 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035962 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035962/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035962 Building REAL250005035963 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035963' /scratch/stefan/7916117/working/building/REAL250005035963 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035963 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035963/0 /scratch/stefan/7916117/working/building/REAL250005035963 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/543 `/scratch/stefan/7916117/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035963.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035963 none COC(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 155, 201, 96, 97, 23, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 149, 149, 114, 114, 101, 101, 22, 8, 7, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 889 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035963 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035963 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035963/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035963 Building REAL250005035964 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035964' /scratch/stefan/7916117/working/building/REAL250005035964 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035964 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035964/0 /scratch/stefan/7916117/working/building/REAL250005035964 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/544 `/scratch/stefan/7916117/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CN=C21) `REAL250005035964.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035964 none CN1N=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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, 67, 67, 67, 23, 8, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 139, 139, 139, 66, 24, 24, 8, 8, 139] 139 rigid atoms, others: [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]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035964 none CN1N=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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, 7, 7, 7, 41, 74, 139, 139, 139, 139, 139, 1, 1, 1, 2, 2, 2, 1, 7, 41, 41, 74, 74, 1] 139 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 24, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035964 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035964 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035964/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035964 Building REAL250005035965 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035965' /scratch/stefan/7916117/working/building/REAL250005035965 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035965 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035965/0 /scratch/stefan/7916117/working/building/REAL250005035965 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/545 `/scratch/stefan/7916117/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C12CCC(CC1)C2) `REAL250005035965.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035965 none O=C(NCCC1=NC(=O)O[N-]1)C12CCC(CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 49, 89, 189, 189, 189, 189, 189, 1, 1, 1, 1, 1, 1, 1, 7, 49, 49, 89, 89, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 189 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 561 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035965 none O=C(NCCC1=NC(=O)O[N-]1)C12CCC(CC1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 19, 8, 1, 1, 1, 1, 1, 1, 1, 49, 189, 189, 189, 189, 189, 189, 49, 20, 19, 8, 8, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189, 189] 189 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035965 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035965 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035965/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035965 Building REAL250005035966 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035966' /scratch/stefan/7916117/working/building/REAL250005035966 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035966 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035966/0 /scratch/stefan/7916117/working/building/REAL250005035966 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/546 `/scratch/stefan/7916117/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[NH2+]C(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035966.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035966 none CCC(C)(C)[NH2+]C(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 9, 6, 6, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 43, 24, 43, 43, 24, 24, 24, 22, 24, 22, 22, 15, 7, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 22, 15, 15, 7, 7] 51 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035966 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035966 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035966/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035966 Building REAL250005035967 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035967' /scratch/stefan/7916117/working/building/REAL250005035967 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035967 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035967/0 /scratch/stefan/7916117/working/building/REAL250005035967 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/547 `/scratch/stefan/7916117/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(F)(F)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035967.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035967 none CC1=CC=C(C(F)(F)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 174, 201, 201, 166, 71, 166, 166, 71, 71, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 71, 19, 19, 8, 8, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 803 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035967 none CC1=CC=C(C(F)(F)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 7, 7, 7, 33, 33, 33, 121, 131, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 33, 121, 121, 131, 131, 1, 1] 201 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: 630 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035967 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035967 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035967/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035967 Building REAL250005035968 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035968' /scratch/stefan/7916117/working/building/REAL250005035968 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035968 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035968/0 /scratch/stefan/7916117/working/building/REAL250005035968 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/548 `/scratch/stefan/7916117/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=N1) `REAL250005035968.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035968 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [13, 1, 13, 13, 53, 63, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 1, 13, 53, 53, 63, 63, 1, 1, 1] 112 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035968 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 22, 8, 1, 1, 1, 1, 1, 1, 1, 75, 112, 112, 112, 112, 112, 112, 75, 22, 22, 8, 8, 112, 112, 112] 112 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035968 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035968 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035968/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035968 Building REAL250005035969 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035969' /scratch/stefan/7916117/working/building/REAL250005035969 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035969 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035969/0 /scratch/stefan/7916117/working/building/REAL250005035969 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/549 `/scratch/stefan/7916117/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C2CC2)=C1) `REAL250005035969.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035969 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 33, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 10, 10, 1, 5, 29, 29, 33, 33, 1, 1, 10, 10, 10, 10, 10, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035969 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 49, 123, 123, 88, 123, 123, 201, 201, 123, 49, 17, 17, 8, 8, 123, 123, 201, 201, 201, 201, 201, 123] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 677 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035969 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 10, 36, 36, 116, 119, 201, 201, 201, 201, 201, 10, 10, 10, 10, 1, 1, 1, 1, 10, 36, 116, 116, 119, 119, 10, 10, 1, 1, 1, 1, 1, 10] 201 rigid atoms, others: [15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 32]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035969 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035969 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035969/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035969 Building REAL250005035970 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035970' /scratch/stefan/7916117/working/building/REAL250005035970 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035970 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035970/0 /scratch/stefan/7916117/working/building/REAL250005035970 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/550 `/scratch/stefan/7916117/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005035970.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035970 none CO[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 4, 4, 19, 19, 19, 73, 89, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 73, 73, 89, 89, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 15, 16, 17, 18, 19, 20, 29, 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]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035970 none CO[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [161, 161, 68, 161, 68, 68, 20, 8, 1, 1, 1, 1, 1, 1, 1, 161, 201, 201, 161, 201, 201, 161, 161, 161, 67, 20, 20, 8, 8, 201, 201, 161, 201, 201] 201 rigid atoms, others: [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, 33]) total number of confs: 786 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035970 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035970 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035970/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035970 Building REAL250005035971 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035971' /scratch/stefan/7916117/working/building/REAL250005035971 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035971 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035971/0 /scratch/stefan/7916117/working/building/REAL250005035971 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/551 `/scratch/stefan/7916117/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1C) `REAL250005035971.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035971 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 116, 140, 140, 91, 91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 140, 140, 140, 140, 91, 24, 24, 8, 8, 140, 140, 140] 140 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 474 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035971 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 41, 67, 140, 140, 140, 140, 140, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 41, 41, 67, 67, 2, 2, 2] 140 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 23, 24] set([32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 405 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035971 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035971 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035971/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035971 Building REAL250005035972 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035972' /scratch/stefan/7916117/working/building/REAL250005035972 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035972 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035972/0 /scratch/stefan/7916117/working/building/REAL250005035972 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/552 `/scratch/stefan/7916117/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035972.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035972 none CC1=NSC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 170, 171, 171, 171, 91, 91, 91, 20, 8, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 91, 20, 20, 8, 8] 171 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 401 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035972 none CC1=NSC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 57, 92, 171, 171, 171, 171, 171, 2, 2, 2, 1, 10, 57, 57, 92, 92] 171 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035972 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035972 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035972/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035972 Building REAL250005035973 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035973' /scratch/stefan/7916117/working/building/REAL250005035973 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035973 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035973/0 /scratch/stefan/7916117/working/building/REAL250005035973 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/553 `/scratch/stefan/7916117/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(ON=C(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035973.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035973 none CCCCC(ON=C(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 8, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 169, 156, 105, 40, 100, 147, 164, 164, 164, 40, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 172, 169, 169, 167, 167, 109, 164, 164, 164, 164, 164, 164, 39, 8, 8, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 946 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035973 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035973 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035973/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035973 Building REAL250005035974 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035974' /scratch/stefan/7916117/working/building/REAL250005035974 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035974 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035974/0 /scratch/stefan/7916117/working/building/REAL250005035974 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/554 `/scratch/stefan/7916117/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCCS1) `REAL250005035974.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035974 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCCS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 1, 13, 13, 73, 115, 195, 195, 195, 195, 195, 1, 1, 1, 1, 1, 1, 13, 74, 74, 115, 115, 1, 1, 1, 1, 1, 1, 1, 1, 1] 195 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) 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: REAL250005035974 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCCS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 99, 195, 195, 195, 195, 195, 99, 25, 25, 8, 8, 195, 195, 195, 195, 195, 195, 195, 195, 195] 195 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 605 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035974 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035974 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035974/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035974 Building REAL250005035975 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035975' /scratch/stefan/7916117/working/building/REAL250005035975 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035975 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035975/0 /scratch/stefan/7916117/working/building/REAL250005035975 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/555 `/scratch/stefan/7916117/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035975.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035975 none CCC(C)CCCCC(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 81, 201, 101, 81, 75, 22, 22, 22, 9, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 101, 101, 101, 101, 75, 75, 22, 9, 9, 5, 5] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035975 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035975 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035975/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035975 Building REAL250005035976 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035976' /scratch/stefan/7916117/working/building/REAL250005035976 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035976 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035976/0 /scratch/stefan/7916117/working/building/REAL250005035976 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/556 `/scratch/stefan/7916117/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCCC1=NNN=C1)NCCC1=NC(=O)O[N-]1) `REAL250005035976.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035976 none O=C(CCCCC1=NNN=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 8, 8, 8, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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, 48, 48, 105, 130, 149, 151, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 149, 149, 149, 149, 151, 151, 201, 201, 48, 17, 17, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 874 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035976 none O=C(CCCCC1=NNN=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 8, 8, 8, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [55, 22, 14, 12, 8, 1, 1, 1, 1, 1, 1, 55, 55, 119, 119, 201, 201, 201, 201, 201, 22, 22, 14, 14, 14, 14, 8, 8, 1, 1, 55, 119, 119, 119, 119] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 642 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035976 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035976/1 /scratch/stefan/7916117/working/building/REAL250005035976 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/557 `/scratch/stefan/7916117/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCCC1=CNN=N1)NCCC1=NC(=O)O[N-]1) `REAL250005035976.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035976 none O=C(CCCCC1=CNN=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 1, 8, 8, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [59, 59, 59, 128, 132, 154, 172, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 154, 154, 154, 154, 172, 172, 201, 201, 59, 17, 17, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 942 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035976 none O=C(CCCCC1=CNN=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 1, 8, 8, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [51, 21, 12, 12, 8, 1, 1, 1, 1, 1, 1, 51, 51, 103, 103, 201, 201, 201, 201, 201, 21, 21, 12, 12, 12, 12, 8, 8, 1, 1, 51, 103, 103, 103, 103] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 598 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035976 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035976 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035976/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035976/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035976 Building REAL250005035977 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035977' /scratch/stefan/7916117/working/building/REAL250005035977 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035977 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035977/0 /scratch/stefan/7916117/working/building/REAL250005035977 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/558 `/scratch/stefan/7916117/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1) `REAL250005035977.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035977 none CC1=CC(C)=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 72, 72, 72, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 23, 23, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [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, 36, 37, 38]) total number of confs: 756 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: REAL250005035977 none CC1=CC(C)=C(CC(=O)NCCC2=NC(=O)O[N-]2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 72, 109, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 2, 18, 72, 72, 109, 109, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 38] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 628 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035977 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035977 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035977/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035977 Building REAL250005035978 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035978' /scratch/stefan/7916117/working/building/REAL250005035978 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035978 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035978/0 /scratch/stefan/7916117/working/building/REAL250005035978 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/559 `/scratch/stefan/7916117/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035978.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035978 none COCCCOCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 163, 138, 116, 89, 46, 46, 46, 15, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 163, 163, 138, 138, 89, 89, 46, 15, 15, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 854 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035978 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035978 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035978/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035978 Building REAL250005035979 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035979' /scratch/stefan/7916117/working/building/REAL250005035979 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035979 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035979/0 /scratch/stefan/7916117/working/building/REAL250005035979 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/560 `/scratch/stefan/7916117/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(CC)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035979.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035979 none CCCCCC(CC)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 166, 123, 112, 76, 33, 76, 84, 33, 33, 8, 8, 1, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 166, 166, 123, 123, 112, 112, 76, 94, 94, 94, 94, 94, 32, 9, 9, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1058 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035979 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035979 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035979/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035979 Building REAL250005035980 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035980' /scratch/stefan/7916117/working/building/REAL250005035980 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035980 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035980/0 /scratch/stefan/7916117/working/building/REAL250005035980 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/561 `/scratch/stefan/7916117/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005035980.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035980 none CC1=CC=C(CC(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 169, 65, 169, 65, 65, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 169, 169, 65, 21, 21, 8, 8, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 849 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035980 none CC1=CC=C(CC(C)C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 6, 6, 28, 28, 28, 107, 116, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 3, 3, 6, 6, 6, 6, 28, 107, 107, 116, 116, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 19, 20, 24, 25, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 583 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035980 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035980 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035980/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035980 Building REAL250005035981 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035981' /scratch/stefan/7916117/working/building/REAL250005035981 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035981 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035981/0 /scratch/stefan/7916117/working/building/REAL250005035981 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/562 `/scratch/stefan/7916117/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOCC1) `REAL250005035981.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035981 none CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 135, 79, 79, 79, 22, 8, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 165, 165, 165, 165, 165, 79, 23, 23, 8, 8, 135, 135, 135, 135, 135, 135, 135, 135] 165 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 651 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035981 none CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 1, 1, 3, 3, 3, 19, 31, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 19, 19, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1] 165 rigid atoms, others: [32, 1, 2, 3, 36, 33, 34, 14, 15, 16, 17, 18, 35, 29, 30, 31] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035981 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035981 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035981/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035981 Building REAL250005035982 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035982' /scratch/stefan/7916117/working/building/REAL250005035982 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035982 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035982/0 /scratch/stefan/7916117/working/building/REAL250005035982 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/563 `/scratch/stefan/7916117/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(=O)N1) `REAL250005035982.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035982 none CC(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', '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, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 195, 195, 74, 74, 74, 20, 8, 1, 1, 1, 1, 1, 1, 1, 195, 195, 195, 195, 201, 201, 201, 201, 201, 201, 201, 195, 73, 20, 20, 8, 8, 195, 195] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 445 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: REAL250005035982 none CC(C)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', '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, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 7, 7, 7, 31, 50, 195, 195, 195, 195, 195, 1, 1, 1, 1, 5, 5, 5, 4, 5, 5, 5, 1, 7, 31, 31, 50, 50, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 17, 18, 19, 20, 28, 35] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 412 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035982 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035982 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035982/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035982 Building REAL250005035983 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035983' /scratch/stefan/7916117/working/building/REAL250005035983 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035983 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035983/0 /scratch/stefan/7916117/working/building/REAL250005035983 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/564 `/scratch/stefan/7916117/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNC=C(C(=O)NCCC2=NC(=O)O[N-]2)C1=O) `REAL250005035983.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035983 none CC1=CNC=C(C(=O)NCCC2=NC(=O)O[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 198, 198, 198, 116, 116, 116, 24, 8, 1, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 198, 198, 198, 198, 116, 25, 25, 8, 8] 198 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 471 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035983 none CC1=CNC=C(C(=O)NCCC2=NC(=O)O[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 79, 111, 198, 198, 198, 198, 198, 1, 1, 2, 2, 2, 1, 1, 1, 13, 79, 79, 111, 111] 198 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 22, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035983 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035983 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035983/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035983 Building REAL250005035984 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035984' /scratch/stefan/7916117/working/building/REAL250005035984 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035984 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035984/0 /scratch/stefan/7916117/working/building/REAL250005035984 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/565 `/scratch/stefan/7916117/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl) `REAL250005035984.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035984 none N#CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 55, 55, 55, 20, 8, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 54, 21, 21, 8, 8, 137, 137] 137 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL250005035984 none N#CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 7, 7, 7, 41, 63, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 7, 41, 41, 63, 63, 1, 1] 137 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035984 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035984 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035984/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035984 Building REAL250005035985 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035985' /scratch/stefan/7916117/working/building/REAL250005035985 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035985 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035985/0 /scratch/stefan/7916117/working/building/REAL250005035985 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/566 `/scratch/stefan/7916117/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C(F)F)C=C1) `REAL250005035985.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035985 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 44, 54, 192, 192, 192, 192, 192, 1, 1, 1, 1, 12, 12, 1, 1, 11, 44, 44, 54, 54, 12, 1, 1] 197 rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 19, 20, 21, 22, 23, 24]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035985 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(C(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 19, 8, 1, 1, 1, 1, 1, 1, 1, 73, 192, 192, 192, 197, 197, 192, 192, 73, 19, 19, 8, 8, 197, 192, 192] 197 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 429 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035985 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035985 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035985/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035985 Building REAL250005035986 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035986' /scratch/stefan/7916117/working/building/REAL250005035986 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035986 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035986/0 /scratch/stefan/7916117/working/building/REAL250005035986 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/567 `/scratch/stefan/7916117/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOCCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035986.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035986 none C=CCCOCCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 114, 66, 66, 66, 62, 54, 19, 19, 19, 11, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 114, 114, 66, 66, 66, 66, 66, 66, 54, 54, 19, 11, 11, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 956 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035986 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035986 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035986/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035986 Building REAL250005035987 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035987' /scratch/stefan/7916117/working/building/REAL250005035987 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005035987 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035987/0 /scratch/stefan/7916117/working/building/REAL250005035987 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/568 `/scratch/stefan/7916117/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC2=C[NH+]=CN21) `REAL250005035987.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035987 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC2=C[NH+]=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 6, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 61, 61, 61, 17, 8, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 61, 17, 17, 8, 8, 93, 93, 93, 93] 93 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL250005035987 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC2=C[NH+]=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 6, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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 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, 7, 7, 7, 33, 43, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 33, 33, 43, 43, 1, 1, 1, 1] 93 rigid atoms, others: [0, 1, 2, 3, 33, 32, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035987 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005035987/1 /scratch/stefan/7916117/working/building/REAL250005035987 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/569 `/scratch/stefan/7916117/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC2=CN=CN21) `REAL250005035987.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005035987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035987 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC2=CN=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 96, 96, 96, 24, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 131, 131, 96, 24, 24, 8, 8, 131, 131, 131, 131] 131 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035987 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CC2=CN=CN21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 42, 70, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 42, 42, 70, 70, 1, 1, 1, 1] 131 rigid atoms, others: [0, 1, 2, 3, 32, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035987 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035987 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035987/0.* 1: /scratch/stefan/7916117/working/building/REAL250005035987/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035987 Building REAL250005035988 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035988' /scratch/stefan/7916117/working/building/REAL250005035988 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035988 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035988/0 /scratch/stefan/7916117/working/building/REAL250005035988 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/570 `/scratch/stefan/7916117/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)N1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL250005035988.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035988 none CCC(C)N1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 165, 197, 165, 165, 109, 109, 109, 24, 8, 1, 1, 1, 1, 1, 1, 1, 166, 166, 166, 201, 201, 201, 201, 201, 197, 197, 197, 197, 108, 24, 24, 8, 8, 166, 166, 166, 166] 201 rigid atoms, others: [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, 36, 37, 38]) total number of confs: 613 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035988 none CCC(C)N1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 1, 8, 8, 8, 32, 54, 165, 165, 165, 166, 166, 1, 1, 1, 7, 7, 7, 7, 7, 3, 4, 4, 4, 8, 31, 31, 54, 54, 1, 2, 2, 2] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 18, 19, 20] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035988 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035988 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035988/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035988 Building REAL250005035989 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035989' /scratch/stefan/7916117/working/building/REAL250005035989 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035989 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035989/0 /scratch/stefan/7916117/working/building/REAL250005035989 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/571 `/scratch/stefan/7916117/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035989.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035989 none COCCCC(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 200, 140, 138, 101, 37, 100, 37, 37, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 140, 140, 137, 138, 102, 102, 100, 102, 36, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 921 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035989 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035989 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035989/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035989 Building REAL250005035990 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035990' /scratch/stefan/7916117/working/building/REAL250005035990 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035990 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035990/0 /scratch/stefan/7916117/working/building/REAL250005035990 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/572 `/scratch/stefan/7916117/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(F)CC1=CC=CC=C1) `REAL250005035990.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035990 none O=C(NCCC1=NC(=O)O[N-]1)C(F)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 33, 33, 118, 127, 201, 201, 201, 201, 201, 2, 7, 1, 1, 1, 1, 1, 1, 1, 33, 118, 118, 127, 127, 7, 2, 2, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL250005035990 none O=C(NCCC1=NC(=O)O[N-]1)C(F)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 8, 1, 1, 1, 1, 1, 1, 1, 74, 165, 165, 194, 201, 201, 194, 201, 201, 73, 23, 22, 8, 8, 165, 194, 194, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 849 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035990 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035990 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035990/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035990 Building REAL250005035991 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035991' /scratch/stefan/7916117/working/building/REAL250005035991 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035991 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035991/0 /scratch/stefan/7916117/working/building/REAL250005035991 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/573 `/scratch/stefan/7916117/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=NOC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035991.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035991 none COC(=O)C1=NOC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 158, 201, 159, 159, 159, 80, 80, 80, 22, 8, 1, 1, 1, 1, 1, 1, 1, 159, 201, 201, 201, 79, 22, 22, 8, 8, 158] 201 rigid atoms, others: [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]) 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: REAL250005035991 none COC(=O)C1=NOC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [9, 9, 1, 9, 1, 1, 1, 1, 1, 8, 8, 8, 42, 63, 159, 159, 159, 159, 159, 1, 9, 9, 9, 9, 41, 41, 63, 63, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 19, 28] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035991 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035991 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035991/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035991 Building REAL250005035992 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035992' /scratch/stefan/7916117/working/building/REAL250005035992 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035992 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035992/0 /scratch/stefan/7916117/working/building/REAL250005035992 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/574 `/scratch/stefan/7916117/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=C1[O-]) `REAL250005035992.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035992 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [6, 1, 6, 6, 16, 16, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 1, 1, 1] 25 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005035992 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 16, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [19, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 19, 25, 25, 25, 25, 25, 25, 25, 19, 8, 8, 8, 8, 25, 25, 25] 25 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035992 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035992 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035992/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035992 Building REAL250005035993 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035993' /scratch/stefan/7916117/working/building/REAL250005035993 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035993 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035993/0 /scratch/stefan/7916117/working/building/REAL250005035993 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/575 `/scratch/stefan/7916117/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035993.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035993 none CCC1=CC=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 114, 114, 113, 113, 113, 79, 79, 79, 24, 8, 1, 1, 1, 1, 1, 1, 1, 114, 201, 201, 201, 201, 201, 113, 113, 78, 25, 25, 8, 8, 114] 201 rigid atoms, others: [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]) total number of confs: 829 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035993 none CCC1=CC=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 38, 45, 113, 113, 113, 113, 113, 1, 6, 6, 6, 5, 5, 1, 1, 10, 38, 38, 45, 45, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 18, 24, 25, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035993 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035993 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035993/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035993 Building REAL250005035994 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035994' /scratch/stefan/7916117/working/building/REAL250005035994 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035994 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035994/0 /scratch/stefan/7916117/working/building/REAL250005035994 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/576 `/scratch/stefan/7916117/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1CC) `REAL250005035994.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035994 none CCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 83, 83, 83, 83, 33, 33, 33, 19, 8, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 194, 172, 172, 172, 172, 172, 83, 83, 33, 19, 19, 8, 8, 83, 194, 194, 194, 194, 194] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1288 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: REAL250005035994 none CCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 37, 83, 83, 83, 83, 83, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 5, 29, 29, 37, 37, 1, 6, 6, 6, 6, 6] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 17, 18, 19, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 241 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035994 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035994 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035994/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035994 Building REAL250005035995 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035995' /scratch/stefan/7916117/working/building/REAL250005035995 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035995 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035995/0 /scratch/stefan/7916117/working/building/REAL250005035995 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/577 `/scratch/stefan/7916117/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C)=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035995.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035995 none CC1=CC=CC(C)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 70, 70, 70, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 24, 24, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 754 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: REAL250005035995 none CC1=CC=CC(C)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 1, 1, 3, 18, 18, 18, 78, 103, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 2, 2, 2, 3, 3, 18, 78, 78, 103, 103] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 578 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035995 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035995 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035995/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035995 Building REAL250005035996 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035996' /scratch/stefan/7916117/working/building/REAL250005035996 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035996 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035996/0 /scratch/stefan/7916117/working/building/REAL250005035996 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/578 `/scratch/stefan/7916117/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC1=CC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035996.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035996 none N#CCC1=CC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 173, 173, 173, 173, 173, 173, 152, 37, 37, 37, 15, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 173, 173, 173, 173, 152, 152, 37, 15, 15, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005035996 none N#CCC1=CC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 21, 21, 21, 82, 86, 173, 173, 173, 173, 173, 6, 6, 1, 1, 1, 1, 3, 3, 21, 82, 82, 86, 86] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035996 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035996 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035996/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035996 Building REAL250005035997 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035997' /scratch/stefan/7916117/working/building/REAL250005035997 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035997 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035997/0 /scratch/stefan/7916117/working/building/REAL250005035997 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/579 `/scratch/stefan/7916117/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005035997.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035997 none CSC1=CC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 175, 175, 175, 175, 175, 175, 117, 37, 37, 37, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 175, 175, 175, 175, 117, 117, 37, 19, 19, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL250005035997 none CSC1=CC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 33, 33, 33, 97, 99, 175, 175, 175, 175, 175, 7, 7, 7, 1, 1, 1, 1, 6, 6, 33, 97, 97, 99, 99] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 520 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035997 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035997 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035997/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035997 Building REAL250005035998 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035998' /scratch/stefan/7916117/working/building/REAL250005035998 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035998 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035998/0 /scratch/stefan/7916117/working/building/REAL250005035998 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/580 `/scratch/stefan/7916117/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005035998.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035998 none CC1=CC(C)=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 1, 1, 1, 5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 199, 201, 201, 201, 199, 173, 64, 64, 64, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 199, 201, 201, 201, 201, 201, 201, 175, 175, 64, 20, 20, 8, 8, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 846 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035998 none CC1=CC(C)=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 1, 1, 1, 5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 23, 23, 23, 92, 107, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 2, 2, 2, 1, 5, 5, 8, 8, 23, 92, 92, 107, 107, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 24, 38, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 606 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035998 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035998 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035998/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035998 Building REAL250005035999 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005035999' /scratch/stefan/7916117/working/building/REAL250005035999 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005035999 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005035999/0 /scratch/stefan/7916117/working/building/REAL250005035999 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/581 `/scratch/stefan/7916117/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1) `REAL250005035999.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005035999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005035999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035999 none CC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 123, 201, 97, 123, 123, 58, 58, 58, 21, 8, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 201, 201, 201, 123, 123, 58, 21, 21, 8, 8, 123] 201 rigid atoms, others: [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]) total number of confs: 668 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005035999 none CC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 1, 1, 1, 1, 1, 12, 12, 12, 42, 46, 123, 123, 123, 123, 123, 1, 1, 1, 9, 9, 9, 1, 1, 12, 42, 42, 46, 46, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 24, 25, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005035999 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005035999 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005035999/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005035999 Building REAL250005036000 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036000' /scratch/stefan/7916117/working/building/REAL250005036000 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036000 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036000/0 /scratch/stefan/7916117/working/building/REAL250005036000 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/582 `/scratch/stefan/7916117/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC(C)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036000.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036000 none COC1=NC(C)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 197, 197, 197, 197, 197, 197, 197, 87, 88, 88, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 197, 197, 197, 197, 197, 87, 20, 20, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036000 none COC1=NC(C)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 68, 98, 197, 197, 197, 197, 197, 4, 4, 4, 2, 2, 2, 1, 1, 12, 68, 68, 98, 98] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036000 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036000 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036000/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036000 Building REAL250005036001 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036001' /scratch/stefan/7916117/working/building/REAL250005036001 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036001 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036001/0 /scratch/stefan/7916117/working/building/REAL250005036001 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/583 `/scratch/stefan/7916117/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CCC)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036001.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036001 none CCCC(CCC)CC(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 137, 80, 137, 186, 186, 17, 17, 17, 7, 5, 1, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 189, 189, 189, 142, 186, 186, 186, 186, 186, 186, 186, 80, 80, 17, 7, 7, 5, 5] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036001 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036001 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036001/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036001 Building REAL250005036002 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036002' /scratch/stefan/7916117/working/building/REAL250005036002 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036002 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036002/0 /scratch/stefan/7916117/working/building/REAL250005036002 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/584 `/scratch/stefan/7916117/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC(F)(F)F)NCCC1=NC(=O)O[N-]1) `REAL250005036002.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036002 none O=C(CCCC(F)(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [55, 55, 55, 183, 195, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 183, 183, 201, 201, 201, 201, 55, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 853 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036002 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036002 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036002/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036002 Building REAL250005036003 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036003' /scratch/stefan/7916117/working/building/REAL250005036003 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036003 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036003/0 /scratch/stefan/7916117/working/building/REAL250005036003 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/585 `/scratch/stefan/7916117/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)CCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036003.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036003 none CSC(C)CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 140, 171, 138, 47, 47, 47, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 171, 171, 171, 171, 150, 150, 138, 138, 47, 17, 17, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 840 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036003 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036003 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036003/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036003 Building REAL250005036004 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036004' /scratch/stefan/7916117/working/building/REAL250005036004 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036004 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036004/0 /scratch/stefan/7916117/working/building/REAL250005036004 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/586 `/scratch/stefan/7916117/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C)C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL250005036004.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036004 none COC1=C(C)C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 12, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 72, 73, 101, 101, 101, 73, 73, 73, 21, 8, 1, 1, 1, 1, 1, 1, 1, 101, 101, 101, 123, 123, 123, 101, 101, 101, 101, 72, 21, 21, 8, 8, 101, 101, 101, 101] 123 rigid atoms, others: [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, 36]) total number of confs: 446 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036004 none COC1=C(C)C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 12, 1, 1, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 26, 38, 101, 101, 101, 101, 101, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 6, 26, 26, 38, 38, 1, 2, 2, 2] 123 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 33, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036004 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036004 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036004/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036004 Building REAL250005036005 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036005' /scratch/stefan/7916117/working/building/REAL250005036005 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036005 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036005/0 /scratch/stefan/7916117/working/building/REAL250005036005 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/587 `/scratch/stefan/7916117/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C=CC=NN21) `REAL250005036005.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036005 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 61, 80, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 61, 61, 80, 80, 1, 1, 1, 1, 1] 160 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 445 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036005 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C=CC=NN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 93, 160, 160, 160, 160, 160, 160, 160, 158, 92, 24, 24, 8, 8, 160, 160, 160, 160, 160] 160 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036005 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036005 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036005/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036005 Building REAL250005036006 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036006' /scratch/stefan/7916117/working/building/REAL250005036006 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036006 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036006/0 /scratch/stefan/7916117/working/building/REAL250005036006 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/588 `/scratch/stefan/7916117/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=N1) `REAL250005036006.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036006 none CC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 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, 96, 96, 96, 24, 8, 1, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 170, 170, 170, 96, 24, 24, 8, 8, 170, 170, 170] 170 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 404 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036006 none CC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 58, 90, 170, 170, 170, 170, 170, 1, 1, 1, 2, 2, 2, 1, 10, 58, 58, 90, 90, 2, 2, 2] 170 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 526 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036006 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036006 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036006/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036006 Building REAL250005036007 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036007' /scratch/stefan/7916117/working/building/REAL250005036007 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036007 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036007/0 /scratch/stefan/7916117/working/building/REAL250005036007 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/589 `/scratch/stefan/7916117/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1O) `REAL250005036007.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036007 none CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 119, 53, 53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 53, 17, 17, 8, 8, 201, 402] 402 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1012 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036007 none CC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 75, 83, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 15, 75, 75, 83, 83, 1, 2] 402 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 17, 18, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 33]) total number of confs: 515 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036007 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036007 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036007/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036007 Building REAL250005036008 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036008' /scratch/stefan/7916117/working/building/REAL250005036008 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036008 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036008/0 /scratch/stefan/7916117/working/building/REAL250005036008 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/590 `/scratch/stefan/7916117/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(=O)N1) `REAL250005036008.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036008 none CCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 106, 106, 106, 44, 44, 44, 19, 8, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 201, 201, 201, 201, 201, 106, 44, 19, 19, 8, 8, 106, 106] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 826 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: REAL250005036008 none CCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 5, 5, 5, 27, 37, 106, 106, 106, 106, 106, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 5, 27, 27, 37, 37, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 16, 17, 18, 19, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 262 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036008 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036008 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036008/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036008 Building REAL250005036009 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036009' /scratch/stefan/7916117/working/building/REAL250005036009 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036009 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036009/0 /scratch/stefan/7916117/working/building/REAL250005036009 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/591 `/scratch/stefan/7916117/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC=CN=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036009.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036009 none C=CCOC1=CC=CN=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 174, 96, 96, 96, 96, 95, 95, 48, 48, 48, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 96, 96, 95, 47, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 484 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036009 none C=CCOC1=CC=CN=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [62, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 24, 24, 95, 95, 95, 95, 95, 62, 62, 62, 27, 27, 1, 1, 1, 5, 24, 24, 24, 24] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036009 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036009 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036009/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036009 Building REAL250005036010 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036010' /scratch/stefan/7916117/working/building/REAL250005036010 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036010 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036010/0 /scratch/stefan/7916117/working/building/REAL250005036010 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/592 `/scratch/stefan/7916117/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C) `REAL250005036010.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036010 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 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, 84, 84, 84, 24, 8, 1, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 182, 182, 182, 182, 84, 24, 24, 8, 8, 182, 182, 182, 182, 182, 182] 182 rigid atoms, others: [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, 33]) total number of confs: 410 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: REAL250005036010 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 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, 11, 11, 12, 57, 82, 182, 182, 182, 182, 182, 1, 1, 1, 1, 2, 2, 2, 1, 12, 57, 57, 82, 82, 2, 2, 2, 2, 2, 2] 182 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 519 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036010 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036010 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036010/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036010 Building REAL250005036011 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036011' /scratch/stefan/7916117/working/building/REAL250005036011 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036011 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036011/0 /scratch/stefan/7916117/working/building/REAL250005036011 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/593 `/scratch/stefan/7916117/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C=CNC2=N1) `REAL250005036011.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036011 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [12, 1, 12, 12, 49, 61, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 49, 49, 61, 61, 1, 1, 1, 1, 1] 103 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 308 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036011 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C=CNC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [65, 65, 23, 8, 1, 1, 1, 1, 1, 1, 1, 65, 103, 103, 103, 102, 103, 103, 103, 103, 65, 23, 23, 8, 8, 103, 103, 103, 103, 103] 103 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036011 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036011 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036011/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036011 Building REAL250005036012 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036012' /scratch/stefan/7916117/working/building/REAL250005036012 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036012 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036012/0 /scratch/stefan/7916117/working/building/REAL250005036012 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/594 `/scratch/stefan/7916117/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CN=C21) `REAL250005036012.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036012 none CN1C=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 136, 136, 75, 75, 75, 23, 8, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 136, 136, 136, 136, 74, 23, 23, 8, 8, 136] 136 rigid atoms, others: [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]) 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: REAL250005036012 none CN1C=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 43, 78, 136, 136, 136, 136, 136, 1, 1, 1, 2, 2, 2, 1, 1, 7, 43, 43, 78, 78, 1] 136 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 24, 25, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036012 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036012 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036012/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036012 Building REAL250005036013 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036013' /scratch/stefan/7916117/working/building/REAL250005036013 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036013 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036013/0 /scratch/stefan/7916117/working/building/REAL250005036013 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/595 `/scratch/stefan/7916117/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005036013.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036013 none N#CCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [8, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [8, 8, 3, 1, 3, 12, 12, 12, 51, 65, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 1, 8, 8, 3, 12, 51, 51, 65, 65, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 3, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036013 none N#CCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [8, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [178, 178, 121, 69, 69, 69, 22, 8, 1, 1, 1, 1, 1, 1, 1, 121, 153, 153, 144, 153, 153, 178, 178, 121, 68, 22, 22, 8, 8, 153, 153, 128, 153, 153] 201 rigid atoms, others: [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, 33]) total number of confs: 864 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036013 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036013 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036013/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036013 Building REAL250005036014 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036014' /scratch/stefan/7916117/working/building/REAL250005036014 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036014 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036014/0 /scratch/stefan/7916117/working/building/REAL250005036014 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/596 `/scratch/stefan/7916117/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036014.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036014 none CCC1=NN(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [197, 161, 161, 161, 160, 160, 160, 89, 89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 197, 201, 201, 201, 201, 161, 161, 161, 160, 88, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 650 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: REAL250005036014 none CCC1=NN(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 46, 60, 160, 160, 160, 161, 161, 5, 5, 5, 5, 5, 2, 2, 2, 1, 9, 46, 46, 60, 60] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 400 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036014 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036014 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036014/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036014 Building REAL250005036015 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036015' /scratch/stefan/7916117/working/building/REAL250005036015 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036015 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036015/0 /scratch/stefan/7916117/working/building/REAL250005036015 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/597 `/scratch/stefan/7916117/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NN1C(C)C) `REAL250005036015.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036015 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 85, 85, 85, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 22, 22, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 442 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: REAL250005036015 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 58, 83, 201, 201, 201, 201, 201, 1, 1, 1, 1, 4, 4, 2, 2, 2, 12, 58, 58, 83, 83, 1, 4, 4, 4, 4, 4, 4, 4] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 529 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036015 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036015 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036015/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036015 Building REAL250005036016 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036016' /scratch/stefan/7916117/working/building/REAL250005036016 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036016 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036016/0 /scratch/stefan/7916117/working/building/REAL250005036016 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/598 `/scratch/stefan/7916117/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(Cl)(Cl)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036016.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036016 none CC(Cl)(Cl)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'Cl', 'Cl', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 16, 16, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 113, 201, 201, 113, 113, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 113, 24, 24, 8, 8] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036016 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036016 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036016/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036016 Building REAL250005036017 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036017' /scratch/stefan/7916117/working/building/REAL250005036017 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036017 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036017/0 /scratch/stefan/7916117/working/building/REAL250005036017 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/599 `/scratch/stefan/7916117/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N(C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036017.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036017 none COCC(=O)N(C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 195, 113, 113, 113, 97, 113, 40, 40, 40, 11, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 195, 113, 113, 113, 97, 97, 40, 11, 11, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 855 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036017 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036017 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036017/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036017 Building REAL250005036018 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036018' /scratch/stefan/7916117/working/building/REAL250005036018 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036018 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036018/0 /scratch/stefan/7916117/working/building/REAL250005036018 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/600 `/scratch/stefan/7916117/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl) `REAL250005036018.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036018 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 176, 176, 176, 76, 76, 76, 23, 8, 1, 1, 1, 1, 1, 1, 1, 176, 176, 176, 176, 201, 201, 201, 176, 76, 23, 23, 8, 8, 176, 176] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 443 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036018 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 5, 5, 5, 29, 53, 176, 176, 176, 176, 176, 1, 1, 1, 1, 4, 4, 4, 1, 5, 29, 29, 53, 53, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 23, 29, 30] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036018 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036018 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036018/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036018 Building REAL250005036019 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036019' /scratch/stefan/7916117/working/building/REAL250005036019 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036019 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036019/0 /scratch/stefan/7916117/working/building/REAL250005036019 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/601 `/scratch/stefan/7916117/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005036019.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036019 none CN(C)C1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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, 182, 194, 182, 182, 182, 102, 102, 102, 24, 8, 1, 1, 1, 1, 1, 1, 1, 182, 182, 194, 194, 194, 194, 194, 194, 182, 101, 24, 24, 8, 8, 182] 194 rigid atoms, others: [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]) total number of confs: 471 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036019 none CN(C)C1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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: [6, 1, 6, 1, 1, 1, 1, 1, 11, 11, 11, 58, 80, 182, 182, 182, 182, 182, 1, 1, 6, 6, 6, 6, 6, 6, 1, 11, 57, 57, 80, 80, 1] 194 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 18, 19, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036019 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036019 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036019/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036019 Building REAL250005036020 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036020' /scratch/stefan/7916117/working/building/REAL250005036020 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036020 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036020/0 /scratch/stefan/7916117/working/building/REAL250005036020 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/602 `/scratch/stefan/7916117/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NN(CC(=O)NCCC2=NC(=O)O[N-]2)C1=O) `REAL250005036020.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036020 none CN1C=NN(CC(=O)NCCC2=NC(=O)O[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 156, 62, 62, 62, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 156, 156, 62, 20, 20, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL250005036020 none CN1C=NN(CC(=O)NCCC2=NC(=O)O[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 31, 31, 31, 114, 127, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 5, 5, 31, 114, 114, 127, 127] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 17, 18, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036020 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036020 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036020/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036020 Building REAL250005036021 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036021' /scratch/stefan/7916117/working/building/REAL250005036021 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036021 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036021/0 /scratch/stefan/7916117/working/building/REAL250005036021 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/603 `/scratch/stefan/7916117/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C(Cl)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036021.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036021 none CCC1=NN(C)C(Cl)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 144, 144, 144, 144, 144, 144, 144, 62, 62, 62, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 144, 144, 144, 62, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036021 none CCC1=NN(C)C(Cl)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 33, 43, 144, 144, 144, 144, 144, 6, 6, 6, 5, 5, 2, 2, 2, 6, 33, 33, 43, 43] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036021 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036021 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036021/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036021 Building REAL250005036022 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036022' /scratch/stefan/7916117/working/building/REAL250005036022 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036022 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036022/0 /scratch/stefan/7916117/working/building/REAL250005036022 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/604 `/scratch/stefan/7916117/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(C2CC2C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005036022.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036022 none N#CC1=CC=C(C2CC2C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 9, 9, 9, 46, 74, 164, 164, 164, 164, 164, 4, 4, 4, 4, 1, 1, 1, 1, 9, 46, 46, 74, 74, 4, 4] 172 rigid atoms, others: [5, 6, 7, 8, 9, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 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: 449 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: REAL250005036022 none N#CC1=CC=C(C2CC2C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 55, 79, 154, 154, 154, 154, 154, 1, 1, 1, 1, 5, 5, 5, 5, 15, 55, 55, 79, 79, 1, 1] 154 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 20, 21, 22, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 445 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036022 none N#CC1=CC=C(C2CC2C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 172, 164, 164, 164, 88, 88, 88, 24, 8, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 164, 164, 164, 164, 88, 25, 25, 8, 8, 172, 172] 172 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 533 number of broken/clashed sets: 33 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036022 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036022 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036022/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036022 Building REAL250005036023 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036023' /scratch/stefan/7916117/working/building/REAL250005036023 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036023 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036023/0 /scratch/stefan/7916117/working/building/REAL250005036023 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/605 `/scratch/stefan/7916117/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CNC2=NC=NC2=C1) `REAL250005036023.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036023 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNC2=NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 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: [7, 1, 7, 7, 45, 74, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 45, 45, 74, 74, 1, 1, 1, 1] 135 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036023 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNC2=NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 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: [72, 72, 23, 8, 1, 1, 1, 1, 1, 1, 1, 72, 135, 135, 135, 135, 135, 135, 135, 135, 72, 24, 24, 8, 8, 135, 135, 135, 135] 135 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036023 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036023/1 /scratch/stefan/7916117/working/building/REAL250005036023 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/606 `/scratch/stefan/7916117/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C2NC=NC2=C1) `REAL250005036023.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036023 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C2NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 4, 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: [7, 1, 7, 7, 44, 76, 140, 140, 140, 140, 140, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 44, 44, 76, 76, 1, 1, 1, 1] 140 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 439 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036023 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C2NC=NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 4, 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: [70, 70, 24, 8, 1, 1, 1, 1, 1, 1, 1, 70, 140, 140, 140, 140, 140, 140, 140, 140, 70, 24, 24, 8, 8, 140, 140, 140, 140] 140 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036023 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036023 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036023/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036023/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036023 Building REAL250005036024 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036024' /scratch/stefan/7916117/working/building/REAL250005036024 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036024 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036024/0 /scratch/stefan/7916117/working/building/REAL250005036024 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/607 `/scratch/stefan/7916117/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N=N1) `REAL250005036024.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036024 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 108, 108, 108, 24, 8, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 190, 190, 190, 190, 190, 108, 25, 25, 8, 8, 190, 190, 190] 190 rigid atoms, others: [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]) total number of confs: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036024 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 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, 10, 10, 10, 52, 82, 190, 190, 190, 190, 190, 1, 1, 1, 1, 2, 2, 2, 1, 10, 52, 52, 82, 82, 2, 2, 2] 190 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036024 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036024 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036024/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036024 Building REAL250005036025 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036025' /scratch/stefan/7916117/working/building/REAL250005036025 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036025 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036025/0 /scratch/stefan/7916117/working/building/REAL250005036025 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/608 `/scratch/stefan/7916117/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC([N+](=O)[O-])=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036025.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036025 none CN1N=CC([N+](=O)[O-])=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 8, 11, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 166, 166, 166, 166, 93, 93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 92, 24, 24, 8, 8] 166 rigid atoms, others: [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]) total number of confs: 400 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: REAL250005036025 none CN1N=CC([N+](=O)[O-])=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 8, 11, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 53, 76, 166, 166, 166, 166, 166, 2, 2, 2, 1, 11, 53, 53, 76, 76] 166 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: 465 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036025 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036025 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036025/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036025 Building REAL250005036026 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036026' /scratch/stefan/7916117/working/building/REAL250005036026 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036026 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036026/0 /scratch/stefan/7916117/working/building/REAL250005036026 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/609 `/scratch/stefan/7916117/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)N1C=NC=N1) `REAL250005036026.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036026 none CC(C(=O)NCCC1=NC(=O)O[N-]1)N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 42, 42, 42, 113, 122, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 9, 9, 9, 9, 42, 113, 113, 122, 122, 1, 1] 201 rigid atoms, others: [1, 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]) 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: REAL250005036026 none CC(C(=O)NCCC1=NC(=O)O[N-]1)N1C=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [173, 65, 65, 65, 19, 8, 1, 1, 1, 1, 1, 1, 1, 173, 201, 201, 201, 201, 173, 173, 173, 173, 65, 19, 19, 8, 8, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036026 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036026 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036026/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036026 Building REAL250005036027 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036027' /scratch/stefan/7916117/working/building/REAL250005036027 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036027 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036027/0 /scratch/stefan/7916117/working/building/REAL250005036027 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/610 `/scratch/stefan/7916117/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(N(C)C)=N1) `REAL250005036027.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036027 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(N(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 88, 88, 89, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 20, 20, 8, 8, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 432 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036027 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(N(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 57, 86, 201, 201, 201, 201, 201, 1, 1, 1, 6, 6, 1, 2, 2, 2, 9, 57, 57, 86, 86, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036027 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036027 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036027/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036027 Building REAL250005036028 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036028' /scratch/stefan/7916117/working/building/REAL250005036028 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036028 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036028/0 /scratch/stefan/7916117/working/building/REAL250005036028 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/611 `/scratch/stefan/7916117/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(C)(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036028.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036028 none CCOC(=O)C(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 178, 178, 83, 178, 35, 83, 83, 35, 35, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 83, 83, 83, 83, 83, 83, 35, 15, 15, 7, 7] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 783 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036028 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036028 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036028/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036028 Building REAL250005036029 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036029' /scratch/stefan/7916117/working/building/REAL250005036029 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036029 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036029/0 /scratch/stefan/7916117/working/building/REAL250005036029 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/612 `/scratch/stefan/7916117/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)NC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005036029.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036029 none CC1=C(C)NC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 88, 22, 22, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 432 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036029 none CC1=C(C)NC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 78, 113, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 12, 78, 78, 113, 113] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036029 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036029 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036029/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036029 Building REAL250005036030 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036030' /scratch/stefan/7916117/working/building/REAL250005036030 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036030 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036030/0 /scratch/stefan/7916117/working/building/REAL250005036030 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/613 `/scratch/stefan/7916117/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C2=COC=C2)=C1) `REAL250005036030.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036030 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C2=COC=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 28, 32, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 5, 28, 28, 32, 32, 1, 1, 1, 5, 5, 5, 1] 201 rigid atoms, others: [1, 33, 11, 12, 13, 14, 15, 16, 21, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036030 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C2=COC=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 1, 1, 1, 1, 1, 1, 44, 116, 116, 116, 116, 116, 201, 201, 201, 201, 116, 44, 17, 17, 8, 8, 116, 116, 116, 201, 201, 201, 116] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 441 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036030 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C2=COC=C2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 17, 17, 85, 93, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 17, 85, 85, 93, 93, 5, 5, 5, 1, 1, 1, 5] 201 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 512 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036030 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036030 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036030/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036030 Building REAL250005036031 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036031' /scratch/stefan/7916117/working/building/REAL250005036031 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036031 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036031/0 /scratch/stefan/7916117/working/building/REAL250005036031 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/614 `/scratch/stefan/7916117/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1F) `REAL250005036031.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036031 none COC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 165, 165, 165, 165, 165, 77, 77, 77, 22, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 201, 201, 201, 165, 165, 165, 77, 22, 22, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 450 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036031 none COC1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 53, 65, 165, 165, 165, 165, 165, 1, 1, 3, 3, 3, 1, 1, 1, 13, 53, 53, 65, 65] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 18, 19, 23, 24, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036031 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036031 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036031/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036031 Building REAL250005036032 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036032' /scratch/stefan/7916117/working/building/REAL250005036032 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036032 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036032/0 /scratch/stefan/7916117/working/building/REAL250005036032 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/615 `/scratch/stefan/7916117/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCCCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036032.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036032 none CC(=O)CCCCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 201, 91, 66, 89, 68, 82, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 125, 125, 91, 91, 91, 91, 91, 91, 91, 91, 82, 82, 23, 8, 7, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036032 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036032 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036032/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036032 Building REAL250005036033 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036033' /scratch/stefan/7916117/working/building/REAL250005036033 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036033 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036033/0 /scratch/stefan/7916117/working/building/REAL250005036033 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/616 `/scratch/stefan/7916117/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C(C(=O)NCCC3=NC(=O)O[N-]3)=CN=C2C=C1) `REAL250005036033.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036033 none CC1=CN2C(C(=O)NCCC3=NC(=O)O[N-]3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 84, 84, 84, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 25, 24, 8, 8, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036033 none CC1=CN2C(C(=O)NCCC3=NC(=O)O[N-]3)=CN=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 12, 12, 12, 63, 95, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 63, 63, 95, 95, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 16, 17, 18, 19, 20, 24, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036033 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036033 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036033/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036033 Building REAL250005036034 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036034' /scratch/stefan/7916117/working/building/REAL250005036034 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036034 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036034/0 /scratch/stefan/7916117/working/building/REAL250005036034 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/617 `/scratch/stefan/7916117/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005036034.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036034 none COC(=O)C1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 116, 201, 116, 116, 116, 49, 49, 49, 19, 8, 1, 1, 1, 1, 1, 1, 1, 116, 116, 201, 201, 201, 116, 116, 116, 116, 116, 116, 49, 19, 19, 8, 8, 116, 116, 116, 116] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL250005036034 none COC(=O)C1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 12, 12, 12, 51, 58, 116, 116, 116, 116, 116, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 12, 51, 51, 58, 58, 1, 1, 1, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 38, 37, 19, 20, 24, 25, 26, 27, 28, 29, 36] set([0, 1, 34, 3, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036034 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036034 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036034/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036034 Building REAL250005036035 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036035' /scratch/stefan/7916117/working/building/REAL250005036035 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036035 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036035/0 /scratch/stefan/7916117/working/building/REAL250005036035 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/618 `/scratch/stefan/7916117/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036035.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036035 none COC(=O)C1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 122, 201, 122, 122, 122, 122, 49, 49, 49, 19, 8, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 122, 122, 49, 19, 19, 8, 8, 122] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 585 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036035 none COC(=O)C1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 33, 122, 122, 122, 122, 122, 1, 13, 13, 13, 1, 1, 5, 29, 29, 33, 33, 1] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 20, 24, 25, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036035 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036035 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036035/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036035 Building REAL250005036036 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036036' /scratch/stefan/7916117/working/building/REAL250005036036 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036036 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036036/0 /scratch/stefan/7916117/working/building/REAL250005036036 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/619 `/scratch/stefan/7916117/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005036036.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036036 none CC1(C)CCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 200, 200, 92, 93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 201, 200, 200, 92, 25, 25, 8, 8, 201, 201] 201 rigid atoms, others: [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, 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: REAL250005036036 none CC1(C)CCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 62, 92, 200, 200, 201, 200, 200, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 62, 62, 92, 92, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 37, 38, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036036 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036036 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036036/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036036 Building REAL250005036037 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036037' /scratch/stefan/7916117/working/building/REAL250005036037 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036037 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036037/0 /scratch/stefan/7916117/working/building/REAL250005036037 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/620 `/scratch/stefan/7916117/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1C(C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036037.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036037 none CC1=NNC(C)=C1C(C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 187, 201, 70, 70, 70, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 187, 70, 22, 22, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 815 number of broken/clashed sets: 176 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036037 none CC1=NNC(C)=C1C(C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 4, 4, 11, 31, 31, 31, 107, 111, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 4, 4, 4, 4, 11, 11, 31, 107, 107, 111, 111] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 599 number of broken/clashed sets: 186 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036037 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036037 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036037/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036037 Building REAL250005036038 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036038' /scratch/stefan/7916117/working/building/REAL250005036038 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036038 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036038/0 /scratch/stefan/7916117/working/building/REAL250005036038 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/621 `/scratch/stefan/7916117/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=NNC=C2C1) `REAL250005036038.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036038 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=NNC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 8, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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] 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: [12, 1, 12, 12, 71, 109, 182, 182, 182, 182, 182, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 71, 71, 109, 109, 1, 1, 1, 1, 1, 1, 1, 1, 1] 182 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 574 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: REAL250005036038 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=NNC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 8, 8, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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] 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: [96, 96, 23, 8, 1, 1, 1, 1, 1, 1, 1, 96, 182, 182, 182, 182, 182, 182, 182, 182, 96, 23, 23, 8, 8, 182, 182, 182, 182, 182, 182, 182, 182, 182] 182 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 564 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036038 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036038 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036038/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036038 Building REAL250005036039 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036039' /scratch/stefan/7916117/working/building/REAL250005036039 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036039 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036039/0 /scratch/stefan/7916117/working/building/REAL250005036039 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/622 `/scratch/stefan/7916117/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CN=CC(F)=C1)NCCC1=NC(=O)O[N-]1) `REAL250005036039.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036039 none O=C(CCC1=CN=CC(F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [47, 47, 47, 139, 145, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 139, 139, 145, 145, 201, 201, 201, 47, 17, 17, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036039 none O=C(CCC1=CN=CC(F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 1, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [29, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 122, 126, 201, 201, 201, 201, 201, 7, 7, 3, 3, 1, 1, 1, 29, 122, 122, 126, 126] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 611 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036039 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036039 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036039/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036039 Building REAL250005036040 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036040' /scratch/stefan/7916117/working/building/REAL250005036040 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036040 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036040/0 /scratch/stefan/7916117/working/building/REAL250005036040 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/623 `/scratch/stefan/7916117/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC2CCCCC2C1) `REAL250005036040.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036040 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2CCCCC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 28, 42, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 28, 28, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 95 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) 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: REAL250005036040 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2CCCCC2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [60, 60, 22, 8, 1, 1, 1, 1, 1, 1, 1, 60, 95, 95, 95, 95, 95, 95, 95, 95, 95, 60, 22, 22, 8, 8, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95] 95 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036040 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036040 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036040/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036040 Building REAL250005036041 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036041' /scratch/stefan/7916117/working/building/REAL250005036041 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036041 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036041/0 /scratch/stefan/7916117/working/building/REAL250005036041 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/624 `/scratch/stefan/7916117/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C(F)=C1) `REAL250005036041.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036041 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 39, 62, 122, 122, 122, 122, 122, 1, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 62, 62, 1, 1, 1] 122 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 359 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036041 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 21, 8, 1, 1, 1, 1, 1, 1, 1, 52, 122, 122, 122, 122, 122, 122, 122, 52, 21, 21, 8, 8, 122, 122, 122] 122 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036041 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036041 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036041/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036041 Building REAL250005036042 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036042' /scratch/stefan/7916117/working/building/REAL250005036042 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036042 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036042/0 /scratch/stefan/7916117/working/building/REAL250005036042 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/625 `/scratch/stefan/7916117/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N[C@@H](C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036042.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036042 none COC(=O)N[C@@H](C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 154, 201, 134, 50, 134, 134, 50, 50, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 154, 134, 134, 134, 50, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 790 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036042 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036042 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036042/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036042 Building REAL250005036043 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036043' /scratch/stefan/7916117/working/building/REAL250005036043 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036043 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036043/0 /scratch/stefan/7916117/working/building/REAL250005036043 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/626 `/scratch/stefan/7916117/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005036043.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036043 none N#CCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 136, 83, 184, 184, 82, 82, 83, 23, 8, 1, 1, 1, 1, 1, 1, 1, 184, 184, 201, 201, 184, 184, 82, 23, 23, 8, 8, 184, 184] 201 rigid atoms, others: [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]) total number of confs: 1099 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036043 none N#CCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 31, 53, 184, 184, 184, 184, 184, 1, 1, 4, 4, 1, 1, 6, 31, 31, 53, 53, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 18, 19, 22, 23, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036043 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036043 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036043/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036043 Building REAL250005036044 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036044' /scratch/stefan/7916117/working/building/REAL250005036044 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036044 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036044/0 /scratch/stefan/7916117/working/building/REAL250005036044 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/627 `/scratch/stefan/7916117/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)SCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036044.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036044 none CC(C)(C)SCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 192, 172, 159, 58, 58, 58, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 188, 188, 159, 159, 58, 19, 19, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 927 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036044 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036044 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036044/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036044 Building REAL250005036045 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036045' /scratch/stefan/7916117/working/building/REAL250005036045 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036045 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036045/0 /scratch/stefan/7916117/working/building/REAL250005036045 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/628 `/scratch/stefan/7916117/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1C(C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036045.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036045 none CC1=NOC(C)=C1C(C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 146, 131, 146, 53, 53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 146, 146, 146, 146, 131, 131, 53, 17, 17, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 714 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036045 none CC1=NOC(C)=C1C(C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 38, 38, 38, 111, 112, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 9, 9, 38, 111, 111, 112, 112] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 581 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036045 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036045 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036045/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036045 Building REAL250005036046 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036046' /scratch/stefan/7916117/working/building/REAL250005036046 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036046 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036046/0 /scratch/stefan/7916117/working/building/REAL250005036046 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/629 `/scratch/stefan/7916117/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1CCCC1) `REAL250005036046.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036046 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 13, 13, 13, 61, 76, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 61, 61, 76, 76, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 14, 15, 16, 17, 18, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 491 number of broken/clashed sets: 173 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036046 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 56, 156, 56, 56, 19, 8, 1, 1, 1, 1, 1, 1, 1, 156, 201, 201, 201, 201, 156, 156, 156, 156, 156, 156, 56, 19, 19, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 799 number of broken/clashed sets: 173 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036046 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036046 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036046/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036046 Building REAL250005036047 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036047' /scratch/stefan/7916117/working/building/REAL250005036047 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036047 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036047/0 /scratch/stefan/7916117/working/building/REAL250005036047 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/630 `/scratch/stefan/7916117/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1SCCS1) `REAL250005036047.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036047 none O=C(NCCC1=NC(=O)O[N-]1)C1SCCS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 14, 5, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [13, 1, 13, 13, 79, 122, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 79, 79, 122, 122, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20]) total number of confs: 633 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036047 none O=C(NCCC1=NC(=O)O[N-]1)C1SCCS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 14, 5, 5, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 24, 8, 1, 1, 1, 1, 1, 1, 1, 98, 201, 201, 201, 201, 97, 24, 24, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 600 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036047 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036047 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036047/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036047 Building REAL250005036048 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036048' /scratch/stefan/7916117/working/building/REAL250005036048 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036048 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036048/0 /scratch/stefan/7916117/working/building/REAL250005036048 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/631 `/scratch/stefan/7916117/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C(CC(=O)NCCC1=NC(=O)O[N-]1)OCC) `REAL250005036048.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036048 none C=C(C)C(CC(=O)NCCC1=NC(=O)O[N-]1)OCC NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 124, 163, 113, 48, 48, 48, 18, 8, 1, 1, 1, 1, 1, 1, 1, 124, 179, 200, 163, 163, 163, 163, 163, 124, 113, 113, 47, 19, 18, 8, 8, 200, 200, 200, 200, 200] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 892 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036048 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036048 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036048/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036048 Building REAL250005036049 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036049' /scratch/stefan/7916117/working/building/REAL250005036049 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036049 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036049/0 /scratch/stefan/7916117/working/building/REAL250005036049 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/632 `/scratch/stefan/7916117/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)(CC(=O)NCCC1=NC(=O)O[N-]1)C1CC1) `REAL250005036049.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036049 none CC(O)(CC(=O)NCCC1=NC(=O)O[N-]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [5, 1, 5, 5, 18, 37, 37, 37, 102, 114, 201, 201, 201, 201, 201, 1, 1, 1, 5, 5, 5, 15, 18, 18, 37, 102, 102, 114, 114, 1, 1, 1, 1, 1] 603 rigid atoms, others: [32, 1, 33, 15, 16, 17, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 629 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: REAL250005036049 none CC(O)(CC(=O)NCCC1=NC(=O)O[N-]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [200, 156, 201, 72, 72, 73, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 156, 156, 72, 20, 20, 8, 8, 201, 201, 201, 201, 201] 603 rigid atoms, others: [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, 33]) total number of confs: 1459 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036049 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036049 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036049/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036049 Building REAL250005036050 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036050' /scratch/stefan/7916117/working/building/REAL250005036050 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036050 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036050/0 /scratch/stefan/7916117/working/building/REAL250005036050 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/633 `/scratch/stefan/7916117/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(C1=CC=CC=C1)C1CC1) `REAL250005036050.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036050 none O=C(NCCC1=NC(=O)O[N-]1)C(C1=CC=CC=C1)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 19, 19, 82, 90, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 19, 82, 82, 90, 90, 4, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36]) total number of confs: 529 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036050 none O=C(NCCC1=NC(=O)O[N-]1)C(C1=CC=CC=C1)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 51, 16, 8, 1, 1, 1, 1, 1, 1, 1, 51, 151, 201, 201, 151, 201, 201, 151, 153, 153, 50, 16, 16, 8, 8, 151, 201, 201, 151, 201, 201, 153, 153, 153, 153, 153] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 787 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036050 none O=C(NCCC1=NC(=O)O[N-]1)C(C1=CC=CC=C1)C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 14, 60, 70, 153, 153, 153, 153, 153, 1, 3, 6, 6, 3, 6, 6, 1, 1, 1, 14, 60, 60, 70, 70, 3, 6, 6, 3, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 11, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 416 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036050 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036050 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036050/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036050 Building REAL250005036051 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036051' /scratch/stefan/7916117/working/building/REAL250005036051 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036051 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036051/0 /scratch/stefan/7916117/working/building/REAL250005036051 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/634 `/scratch/stefan/7916117/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC=C1F) `REAL250005036051.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036051 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 17, 17, 17, 69, 94, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 17, 69, 69, 94, 94, 1, 1, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL250005036051 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 83, 83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 24, 24, 8, 8, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 785 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036051 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036051 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036051/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036051 Building REAL250005036052 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036052' /scratch/stefan/7916117/working/building/REAL250005036052 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036052 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036052/0 /scratch/stefan/7916117/working/building/REAL250005036052 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/635 `/scratch/stefan/7916117/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C([N+](=O)[O-])C(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005036052.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036052 none CN1C=C([N+](=O)[O-])C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 11, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 200, 200, 200, 200, 95, 95, 95, 24, 8, 1, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 94, 24, 24, 8, 8] 200 rigid atoms, others: [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]) total number of confs: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036052 none CN1C=C([N+](=O)[O-])C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 11, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 11, 11, 11, 60, 94, 200, 200, 200, 200, 200, 1, 2, 2, 2, 1, 11, 60, 60, 94, 94] 200 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 19, 23] set([5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 574 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036052 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036052 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036052/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036052 Building REAL250005036053 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036053' /scratch/stefan/7916117/working/building/REAL250005036053 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036053 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036053/0 /scratch/stefan/7916117/working/building/REAL250005036053 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/636 `/scratch/stefan/7916117/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036053.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036053 none CCC(CC)C(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 149, 144, 154, 201, 54, 144, 54, 54, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 201, 155, 200, 201, 201, 201, 201, 144, 144, 144, 144, 54, 17, 17, 8, 8] 201 rigid atoms, others: [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, 36, 37]) total number of confs: 1212 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036053 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036053 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036053/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036053 Building REAL250005036054 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036054' /scratch/stefan/7916117/working/building/REAL250005036054 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036054 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036054/0 /scratch/stefan/7916117/working/building/REAL250005036054 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/637 `/scratch/stefan/7916117/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CCC(=O)NCCC2=NC(=O)O[N-]2)C=NN1C) `REAL250005036054.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036054 none CC1=C(CCC(=O)NCCC2=NC(=O)O[N-]2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 140, 138, 52, 52, 52, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 140, 140, 138, 138, 52, 17, 17, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 668 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036054 none CC1=C(CCC(=O)NCCC2=NC(=O)O[N-]2)C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 32, 32, 32, 123, 127, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 6, 6, 10, 10, 32, 125, 125, 127, 127, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 32, 16, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 617 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036054 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036054 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036054/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036054 Building REAL250005036055 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036055' /scratch/stefan/7916117/working/building/REAL250005036055 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036055 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036055/0 /scratch/stefan/7916117/working/building/REAL250005036055 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/638 `/scratch/stefan/7916117/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005036055.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036055 none COC1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 138, 45, 45, 45, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 138, 45, 17, 17, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 774 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036055 none COC1CCC(CC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 29, 29, 29, 89, 91, 201, 201, 201, 201, 201, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 29, 89, 89, 91, 91, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 38, 18, 19, 23, 24, 25, 26, 27, 28, 37, 36] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036055 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036055 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036055/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036055 Building REAL250005036056 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036056' /scratch/stefan/7916117/working/building/REAL250005036056 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036056 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036056/0 /scratch/stefan/7916117/working/building/REAL250005036056 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/639 `/scratch/stefan/7916117/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NCCC2=NC(=O)O[N-]2)CCO1) `REAL250005036056.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036056 none CC1CC(C(=O)NCCC2=NC(=O)O[N-]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 91, 91, 91, 22, 8, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 91, 22, 22, 8, 8, 137, 137, 137, 137] 137 rigid atoms, others: [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, 33]) 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: REAL250005036056 none CC1CC(C(=O)NCCC2=NC(=O)O[N-]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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 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, 7, 7, 7, 40, 62, 137, 137, 137, 137, 137, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 40, 40, 62, 62, 1, 1, 1, 1] 137 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 15, 16, 17, 21, 22, 23, 24, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036056 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036056 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036056/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036056 Building REAL250005036057 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036057' /scratch/stefan/7916117/working/building/REAL250005036057 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036057 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036057/0 /scratch/stefan/7916117/working/building/REAL250005036057 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/640 `/scratch/stefan/7916117/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005036057.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036057 none COCC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 138, 138, 138, 138, 138, 46, 46, 46, 17, 7, 1, 1, 1, 1, 1, 1, 1, 138, 201, 201, 201, 201, 201, 138, 138, 138, 46, 17, 17, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 636 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036057 none COCC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [19, 7, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 42, 46, 138, 138, 138, 138, 138, 1, 19, 19, 19, 7, 7, 2, 2, 2, 9, 42, 42, 46, 46] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 19] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036057 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036057 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036057/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036057 Building REAL250005036058 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036058' /scratch/stefan/7916117/working/building/REAL250005036058 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036058 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036058/0 /scratch/stefan/7916117/working/building/REAL250005036058 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/641 `/scratch/stefan/7916117/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=N1) `REAL250005036058.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036058 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 63, 84, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 1, 13, 63, 63, 84, 84, 1, 1, 1] 151 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 438 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036058 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(F)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 24, 8, 1, 1, 1, 1, 1, 1, 1, 86, 151, 151, 151, 151, 151, 151, 86, 24, 24, 8, 8, 151, 151, 151] 151 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036058 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036058 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036058/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036058 Building REAL250005036059 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036059' /scratch/stefan/7916117/working/building/REAL250005036059 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036059 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036059/0 /scratch/stefan/7916117/working/building/REAL250005036059 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/642 `/scratch/stefan/7916117/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C(=O)NN=C2C=C1) `REAL250005036059.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036059 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C(=O)NN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 4, 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: [7, 1, 7, 7, 41, 61, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 61, 61, 1, 1, 1, 1] 133 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036059 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C(=O)NN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 11, 8, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 4, 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: [68, 68, 22, 8, 1, 1, 1, 1, 1, 1, 1, 68, 133, 133, 133, 133, 133, 133, 133, 133, 133, 67, 22, 22, 8, 8, 133, 133, 133, 133] 133 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036059 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036059 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036059/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036059 Building REAL250005036060 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036060' /scratch/stefan/7916117/working/building/REAL250005036060 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036060 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036060/0 /scratch/stefan/7916117/working/building/REAL250005036060 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/643 `/scratch/stefan/7916117/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)S(=O)(=O)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036060.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036060 none CC(C)(C)S(=O)(=O)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 199, 201, 201, 90, 90, 90, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 90, 23, 23, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 797 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036060 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036060 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036060/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036060 Building REAL250005036061 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036061' /scratch/stefan/7916117/working/building/REAL250005036061 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036061 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036061/0 /scratch/stefan/7916117/working/building/REAL250005036061 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/644 `/scratch/stefan/7916117/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005036061.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036061 none C=CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 98, 141, 141, 97, 97, 98, 24, 8, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 141, 141, 97, 24, 24, 8, 8, 141, 141] 141 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 584 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036061 none C=CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 34, 56, 141, 141, 141, 141, 141, 1, 1, 6, 6, 6, 1, 1, 7, 34, 34, 56, 56, 1, 1] 141 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 22, 23, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 371 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036061 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036061 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036061/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036061 Building REAL250005036062 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036062' /scratch/stefan/7916117/working/building/REAL250005036062 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036062 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036062/0 /scratch/stefan/7916117/working/building/REAL250005036062 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/645 `/scratch/stefan/7916117/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1) `REAL250005036062.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036062 none CCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 13, 13, 13, 58, 67, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 4, 13, 58, 58, 67, 67, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 35, 34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 419 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036062 none CCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 124, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 124, 159, 159, 124, 159, 159, 159, 162, 162, 162, 162, 162, 124, 48, 17, 17, 8, 8, 159, 159, 159, 159] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 933 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036062 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036062 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036062/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036062 Building REAL250005036063 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036063' /scratch/stefan/7916117/working/building/REAL250005036063 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036063 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036063/0 /scratch/stefan/7916117/working/building/REAL250005036063 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/646 `/scratch/stefan/7916117/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(O)C(F)=C1) `REAL250005036063.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036063 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(O)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 224 conformations in input total number of sets (complete confs): 224 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 37, 58, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 58, 58, 1, 1, 2, 1] 224 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 26]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036063 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(O)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 224 conformations in input total number of sets (complete confs): 224 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 22, 8, 1, 1, 1, 1, 1, 1, 1, 49, 112, 112, 112, 112, 112, 112, 112, 49, 22, 22, 8, 8, 112, 112, 224, 112] 224 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036063 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036063/1 /scratch/stefan/7916117/working/building/REAL250005036063 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/647 `/scratch/stefan/7916117/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([O-])C(F)=C1) `REAL250005036063.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036063 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([O-])C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 40, 58, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 1, 1, 1, 7, 40, 40, 58, 58, 1, 1, 1] 111 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 318 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036063 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([O-])C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 22, 8, 1, 1, 1, 1, 1, 1, 1, 48, 111, 111, 111, 111, 111, 111, 111, 47, 22, 22, 8, 8, 111, 111, 111] 111 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036063 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036063 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036063/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036063/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036063 Building REAL250005036064 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036064' /scratch/stefan/7916117/working/building/REAL250005036064 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036064 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036064/0 /scratch/stefan/7916117/working/building/REAL250005036064 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/648 `/scratch/stefan/7916117/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1) `REAL250005036064.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036064 none CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 143, 91, 91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 173, 173, 173, 173, 173, 91, 24, 24, 8, 8, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143] 173 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 659 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036064 none CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 3, 3, 3, 19, 31, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 19, 19, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 173 rigid atoms, others: [32, 1, 2, 3, 36, 37, 38, 33, 34, 14, 15, 16, 17, 18, 35, 29, 30, 31] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036064 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036064 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036064/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036064 Building REAL250005036065 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036065' /scratch/stefan/7916117/working/building/REAL250005036065 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036065 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036065/0 /scratch/stefan/7916117/working/building/REAL250005036065 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/649 `/scratch/stefan/7916117/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCCC1=NC(=O)O[N-]1)C1CCC(C)CC1) `REAL250005036065.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036065 none CCC(C(=O)NCCC1=NC(=O)O[N-]1)C1CCC(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 8, 22, 22, 22, 77, 93, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 8, 22, 77, 77, 93, 93, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 35, 36, 37, 41, 42, 43, 44, 34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 565 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036065 none CCC(C(=O)NCCC1=NC(=O)O[N-]1)C1CCC(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 167, 72, 72, 72, 22, 8, 1, 1, 1, 1, 1, 1, 1, 167, 201, 201, 201, 201, 201, 192, 182, 182, 182, 182, 182, 167, 71, 22, 22, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 923 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036065 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036065 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036065/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036065 Building REAL250005036066 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036066' /scratch/stefan/7916117/working/building/REAL250005036066 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036066 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036066/0 /scratch/stefan/7916117/working/building/REAL250005036066 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/650 `/scratch/stefan/7916117/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C=CC(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005036066.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036066 none CCC1=CC=C(C=CC(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 157, 157, 157, 157, 151, 151, 61, 61, 61, 19, 8, 1, 1, 1, 1, 1, 1, 1, 157, 201, 201, 201, 201, 201, 157, 157, 151, 150, 60, 19, 19, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036066 none CCC1=CC=C(C=CC(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [8, 1, 1, 1, 1, 1, 1, 4, 4, 18, 18, 18, 61, 64, 156, 156, 156, 157, 156, 1, 8, 8, 8, 8, 8, 1, 1, 4, 4, 18, 61, 61, 64, 64] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036066 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036066 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036066/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036066 Building REAL250005036067 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036067' /scratch/stefan/7916117/working/building/REAL250005036067 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036067 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036067/0 /scratch/stefan/7916117/working/building/REAL250005036067 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/651 `/scratch/stefan/7916117/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1Cl) `REAL250005036067.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036067 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 183, 183, 183, 183, 89, 89, 89, 20, 8, 1, 1, 1, 1, 1, 1, 1, 183, 183, 183, 201, 201, 201, 183, 183, 88, 20, 20, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036067 none COC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 45, 55, 183, 183, 183, 183, 183, 1, 1, 1, 4, 4, 4, 1, 1, 12, 45, 45, 55, 55] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 19, 23, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036067 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036067 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036067/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036067 Building REAL250005036068 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036068' /scratch/stefan/7916117/working/building/REAL250005036068 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036068 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036068/0 /scratch/stefan/7916117/working/building/REAL250005036068 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/652 `/scratch/stefan/7916117/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036068.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036068 none CC(C)(O)C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 543 conformations in input total number of sets (complete confs): 543 using faster count positions algorithm for large data unique positions, atoms: [179, 169, 181, 181, 81, 171, 171, 81, 81, 21, 8, 1, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 181, 543, 81, 21, 21, 8, 8] 543 rigid atoms, others: [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]) total number of confs: 1304 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036068 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036068 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036068/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036068 Building REAL250005036069 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036069' /scratch/stefan/7916117/working/building/REAL250005036069 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036069 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036069/0 /scratch/stefan/7916117/working/building/REAL250005036069 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/653 `/scratch/stefan/7916117/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005036069.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036069 none CC(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', '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, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 179, 201, 179, 179, 179, 89, 89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 179, 201, 201, 201, 201, 201, 201, 201, 179, 179, 89, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 544 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036069 none CC(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', '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, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [4, 1, 4, 1, 1, 1, 1, 1, 12, 12, 12, 54, 76, 179, 179, 179, 179, 179, 1, 5, 5, 5, 4, 5, 5, 5, 1, 1, 12, 54, 54, 76, 76] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 477 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036069 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036069 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036069/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036069 Building REAL250005036070 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036070' /scratch/stefan/7916117/working/building/REAL250005036070 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036070 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036070/0 /scratch/stefan/7916117/working/building/REAL250005036070 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/654 `/scratch/stefan/7916117/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC=CC(Cl)=C1[O-]) `REAL250005036070.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036070 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 16, 1, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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: [10, 1, 10, 10, 20, 20, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 10, 20, 20, 20, 20, 1, 1] 31 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005036070 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 16, 1, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 3, 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: [21, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 21, 31, 31, 31, 31, 31, 31, 31, 21, 8, 8, 8, 8, 31, 31] 31 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036070 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036070 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036070/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036070 Building REAL250005036071 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036071' /scratch/stefan/7916117/working/building/REAL250005036071 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036071 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036071/0 /scratch/stefan/7916117/working/building/REAL250005036071 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/655 `/scratch/stefan/7916117/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1) `REAL250005036071.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036071 none CN(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 194, 201, 194, 194, 194, 98, 98, 98, 24, 8, 1, 1, 1, 1, 1, 1, 1, 194, 194, 201, 201, 201, 201, 201, 201, 194, 194, 98, 24, 24, 8, 8, 194] 201 rigid atoms, others: [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]) total number of confs: 470 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036071 none CN(C)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 13, 70, 98, 194, 194, 194, 194, 194, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 13, 70, 70, 98, 98, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 33, 18, 19, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 544 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036071 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036071 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036071/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036071 Building REAL250005036072 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036072' /scratch/stefan/7916117/working/building/REAL250005036072 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036072 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036072/0 /scratch/stefan/7916117/working/building/REAL250005036072 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/656 `/scratch/stefan/7916117/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(CC(=O)NCCC2=NC(=O)O[N-]2)CC1=O) `REAL250005036072.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036072 none CN1CCN(CC(=O)NCCC2=NC(=O)O[N-]2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 186, 73, 74, 74, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 186, 186, 73, 21, 21, 8, 8, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 732 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036072 none CN1CCN(CC(=O)NCCC2=NC(=O)O[N-]2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 27, 27, 27, 94, 101, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 7, 27, 94, 94, 101, 101, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 34, 17, 18, 35, 23, 24, 25, 26] set([32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036072 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036072 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036072/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036072 Building REAL250005036073 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036073' /scratch/stefan/7916117/working/building/REAL250005036073 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036073 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036073/0 /scratch/stefan/7916117/working/building/REAL250005036073 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/657 `/scratch/stefan/7916117/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2SC=CC2=CC=C1) `REAL250005036073.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036073 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2SC=CC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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, 1, 12, 12, 73, 99, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 73, 73, 99, 99, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) 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: REAL250005036073 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2SC=CC2=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [80, 80, 22, 8, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 201, 201, 79, 22, 22, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 424 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036073 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036073 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036073/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036073 Building REAL250005036074 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036074' /scratch/stefan/7916117/working/building/REAL250005036074 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036074 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036074/0 /scratch/stefan/7916117/working/building/REAL250005036074 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/658 `/scratch/stefan/7916117/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005036074.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036074 none CC1CCN(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 146, 79, 146, 79, 79, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 19, 19, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [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, 36]) 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: REAL250005036074 none CC1CCN(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 7, 7, 27, 27, 27, 91, 99, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 27, 91, 91, 99, 99, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 33, 34, 18, 19, 23, 24, 25, 26, 27, 36] set([32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036074 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036074 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036074/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036074 Building REAL250005036075 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036075' /scratch/stefan/7916117/working/building/REAL250005036075 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036075 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036075/0 /scratch/stefan/7916117/working/building/REAL250005036075 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/659 `/scratch/stefan/7916117/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCOC2) `REAL250005036075.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036075 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCOC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 48, 72, 154, 154, 154, 154, 154, 1, 1, 1, 1, 1, 1, 1, 9, 48, 48, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1] 154 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 429 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: REAL250005036075 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCOC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 12, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 91, 154, 154, 154, 154, 154, 154, 90, 25, 25, 8, 8, 154, 154, 154, 154, 154, 154, 154, 154, 154] 154 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 494 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036075 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036075 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036075/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036075 Building REAL250005036076 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036076' /scratch/stefan/7916117/working/building/REAL250005036076 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036076 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036076/0 /scratch/stefan/7916117/working/building/REAL250005036076 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/660 `/scratch/stefan/7916117/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCN(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005036076.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036076 none CC1CCCN(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 152, 75, 152, 75, 75, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 19, 19, 8, 8, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 571 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036076 none CC1CCCN(C(=O)C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 7, 7, 27, 29, 29, 92, 96, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 29, 92, 92, 96, 96, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 36, 19, 23, 24, 25, 26, 27, 28, 29, 35] set([32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 30, 31]) total number of confs: 528 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036076 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036076 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036076/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036076 Building REAL250005036077 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036077' /scratch/stefan/7916117/working/building/REAL250005036077 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036077 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036077/0 /scratch/stefan/7916117/working/building/REAL250005036077 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/661 `/scratch/stefan/7916117/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCCCC1OCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036077.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036077 none CCC1CCCCC1OCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 197, 197, 197, 197, 153, 46, 46, 47, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 197, 197, 197, 197, 197, 197, 197, 197, 157, 157, 46, 8, 8, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 649 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036077 none CCC1CCCCC1OCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 55, 55, 55, 123, 123, 197, 197, 197, 197, 197, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 55, 123, 123, 123, 123] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 35, 26, 27, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036077 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036077 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036077/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036077 Building REAL250005036078 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036078' /scratch/stefan/7916117/working/building/REAL250005036078 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036078 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036078/0 /scratch/stefan/7916117/working/building/REAL250005036078 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/662 `/scratch/stefan/7916117/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([O-])C([N+](=O)[O-])=C1) `REAL250005036078.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036078 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 38, 58, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 38, 38, 58, 58, 1, 1, 1] 134 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 358 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036078 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([O-])C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 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: [57, 57, 24, 8, 1, 1, 1, 1, 1, 1, 1, 57, 134, 134, 100, 134, 134, 134, 134, 134, 134, 56, 24, 24, 8, 8, 134, 134, 134] 134 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036078 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036078 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036078/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036078 Building REAL250005036079 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036079' /scratch/stefan/7916117/working/building/REAL250005036079 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036079 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036079/0 /scratch/stefan/7916117/working/building/REAL250005036079 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/663 `/scratch/stefan/7916117/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)[C@@H]1C[C@H](CC(=O)NCCC2=NC(=O)O[N-]2)C1(C)C) `REAL250005036079.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036079 none CC(=O)[C@@H]1C[C@H](CC(=O)NCCC2=NC(=O)O[N-]2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 11, 5, 7, 5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 201, 171, 171, 171, 142, 171, 49, 49, 49, 17, 9, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 201, 201, 201, 171, 171, 142, 142, 49, 17, 17, 9, 9, 171, 171, 171, 171, 171, 171] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 785 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: REAL250005036079 none CC(=O)[C@@H]1C[C@H](CC(=O)NCCC2=NC(=O)O[N-]2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 11, 5, 7, 5, 5, 7, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 26, 26, 26, 91, 92, 171, 171, 171, 171, 171, 1, 1, 1, 5, 5, 5, 1, 1, 6, 6, 26, 91, 91, 92, 92, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 20, 21, 22, 26, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 483 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036079 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036079 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036079/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036079 Building REAL250005036080 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036080' /scratch/stefan/7916117/working/building/REAL250005036080 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036080 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036080/0 /scratch/stefan/7916117/working/building/REAL250005036080 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/664 `/scratch/stefan/7916117/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CC=NN2N=C1) `REAL250005036080.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036080 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CC=NN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 58, 80, 164, 163, 164, 163, 163, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 58, 58, 81, 81, 1, 1, 1, 1] 164 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 464 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036080 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CC=NN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 24, 8, 1, 1, 1, 1, 1, 1, 1, 92, 164, 164, 164, 164, 164, 164, 164, 164, 91, 24, 24, 8, 8, 163, 164, 164, 164] 164 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036080 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036080 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036080/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036080 Building REAL250005036081 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036081' /scratch/stefan/7916117/working/building/REAL250005036081 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036081 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036081/0 /scratch/stefan/7916117/working/building/REAL250005036081 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/665 `/scratch/stefan/7916117/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(C2CC2)=N1) `REAL250005036081.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036081 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 64, 64, 64, 20, 8, 1, 1, 1, 1, 1, 1, 1, 121, 121, 121, 201, 201, 121, 121, 121, 121, 64, 20, 20, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 577 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036081 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 29, 39, 120, 120, 120, 120, 120, 1, 1, 1, 12, 12, 1, 2, 2, 2, 8, 29, 29, 39, 39, 12, 12, 12, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036081 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 48, 48, 48, 127, 136, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 12, 13, 13, 13, 48, 127, 127, 136, 136, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 635 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036081 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036081 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036081/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036081 Building REAL250005036082 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036082' /scratch/stefan/7916117/working/building/REAL250005036082 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036082 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036082/0 /scratch/stefan/7916117/working/building/REAL250005036082 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/666 `/scratch/stefan/7916117/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C2COCC2=C1)NCCC1=NC(=O)O[N-]1) `REAL250005036082.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036082 none O=C(CC1=CC=C2COCC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 109, 201, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 201, 201, 48, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036082 none O=C(CC1=CC=C2COCC2=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 77, 86, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 15, 77, 77, 86, 86] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 34, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036082 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036082 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036082/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036082 Building REAL250005036083 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036083' /scratch/stefan/7916117/working/building/REAL250005036083 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036083 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036083/0 /scratch/stefan/7916117/working/building/REAL250005036083 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/667 `/scratch/stefan/7916117/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036083.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036083 none CC(CCC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 55, 165, 200, 201, 201, 200, 201, 55, 55, 19, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 55, 19, 19, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 883 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036083 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036083 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036083/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036083 Building REAL250005036084 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036084' /scratch/stefan/7916117/working/building/REAL250005036084 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036084 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036084/0 /scratch/stefan/7916117/working/building/REAL250005036084 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/668 `/scratch/stefan/7916117/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C(F)C=C1) `REAL250005036084.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036084 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 31, 31, 87, 95, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 1, 31, 87, 87, 95, 95, 1, 1, 1, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24]) total number of confs: 536 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036084 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C(F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 19, 8, 1, 1, 1, 1, 1, 1, 1, 73, 139, 139, 201, 201, 201, 201, 201, 201, 73, 19, 19, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036084 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036084 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036084/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036084 Building REAL250005036085 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036085' /scratch/stefan/7916117/working/building/REAL250005036085 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036085 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036085/0 /scratch/stefan/7916117/working/building/REAL250005036085 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/669 `/scratch/stefan/7916117/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036085.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036085 none COCCC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 183, 153, 158, 67, 158, 158, 67, 67, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 183, 183, 183, 183, 158, 158, 158, 158, 158, 158, 67, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 1015 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036085 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036085 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036085/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036085 Building REAL250005036086 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036086' /scratch/stefan/7916117/working/building/REAL250005036086 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036086 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036086/0 /scratch/stefan/7916117/working/building/REAL250005036086 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/670 `/scratch/stefan/7916117/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1C) `REAL250005036086.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036086 none CC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 141, 81, 81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 141, 141, 141, 141, 81, 25, 25, 8, 8, 141, 141, 141] 141 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 353 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036086 none CC1=NC(C)=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 67, 141, 141, 141, 141, 141, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 43, 43, 67, 67, 2, 2, 2] 141 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 421 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036086 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036086 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036086/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036086 Building REAL250005036087 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036087' /scratch/stefan/7916117/working/building/REAL250005036087 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036087 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036087/0 /scratch/stefan/7916117/working/building/REAL250005036087 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/671 `/scratch/stefan/7916117/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21) `REAL250005036087.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036087 none CN1N=NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 112, 112, 112, 58, 58, 58, 24, 8, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 112, 112, 57, 25, 25, 8, 8, 112] 112 rigid atoms, others: [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]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036087 none CN1N=NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 48, 112, 112, 112, 112, 112, 1, 1, 2, 2, 2, 1, 1, 5, 29, 29, 48, 48, 1] 112 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 24, 25, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036087 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036087 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036087/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036087 Building REAL250005036088 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036088' /scratch/stefan/7916117/working/building/REAL250005036088 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036088 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036088/0 /scratch/stefan/7916117/working/building/REAL250005036088 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/672 `/scratch/stefan/7916117/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(CC(=O)NCCC2=NC(=O)O[N-]2)CCO1) `REAL250005036088.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036088 none CC1(C)CC(CC(=O)NCCC2=NC(=O)O[N-]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 165, 55, 55, 55, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 165, 165, 55, 17, 17, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 773 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036088 none CC1(C)CC(CC(=O)NCCC2=NC(=O)O[N-]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 27, 27, 27, 92, 95, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 7, 7, 27, 92, 92, 95, 95, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 17, 18, 19, 36, 26, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 536 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036088 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036088 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036088/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036088 Building REAL250005036089 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036089' /scratch/stefan/7916117/working/building/REAL250005036089 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036089 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036089/0 /scratch/stefan/7916117/working/building/REAL250005036089 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/673 `/scratch/stefan/7916117/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005036089.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036089 none NC(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 114, 114, 114, 72, 72, 72, 23, 8, 1, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 114, 72, 23, 23, 8, 8] 114 rigid atoms, others: [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]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036089 none NC(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 44, 56, 114, 114, 114, 114, 114, 1, 2, 2, 1, 1, 1, 13, 44, 44, 56, 56] 114 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036089 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036089 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036089/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036089 Building REAL250005036090 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036090' /scratch/stefan/7916117/working/building/REAL250005036090 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036090 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036090/0 /scratch/stefan/7916117/working/building/REAL250005036090 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/674 `/scratch/stefan/7916117/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CO1) `REAL250005036090.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036090 none CCC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [199, 141, 141, 141, 88, 88, 88, 24, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 201, 201, 201, 201, 201, 87, 24, 24, 8, 8, 142] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 738 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036090 none CCC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [8, 1, 1, 1, 1, 1, 6, 6, 6, 35, 52, 142, 142, 142, 142, 142, 1, 1, 9, 9, 9, 8, 8, 7, 34, 34, 52, 52, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036090 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036090 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036090/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036090 Building REAL250005036091 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036091' /scratch/stefan/7916117/working/building/REAL250005036091 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036091 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036091/0 /scratch/stefan/7916117/working/building/REAL250005036091 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/675 `/scratch/stefan/7916117/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=NNN=C2C=C1F) `REAL250005036091.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036091 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=NNN=C2C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 8, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 76, 124, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 76, 76, 124, 124, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) 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: REAL250005036091 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=NNN=C2C=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 8, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 24, 8, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 100, 24, 24, 8, 8, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 451 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036091 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036091 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036091/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036091 Building REAL250005036092 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036092' /scratch/stefan/7916117/working/building/REAL250005036092 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036092 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036092/0 /scratch/stefan/7916117/working/building/REAL250005036092 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/676 `/scratch/stefan/7916117/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Cl)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C) `REAL250005036092.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036092 none CC1=CC(Cl)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 139, 145, 145, 145, 92, 92, 92, 24, 8, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 145, 145, 145, 92, 24, 24, 8, 8, 145, 145, 145, 145] 145 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 391 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036092 none CC1=CC(Cl)=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 41, 63, 145, 145, 145, 145, 145, 1, 1, 1, 2, 2, 2, 1, 7, 41, 41, 63, 63, 1, 2, 2, 2] 145 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 23, 29] set([32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036092 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036092 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036092/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036092 Building REAL250005036093 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036093' /scratch/stefan/7916117/working/building/REAL250005036093 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036093 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036093/0 /scratch/stefan/7916117/working/building/REAL250005036093 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/677 `/scratch/stefan/7916117/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C=C1C(=O)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036093.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036093 none CC1=CC=C(F)C=C1C(=O)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 127, 61, 127, 61, 61, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 61, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 521 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036093 none CC1=CC=C(F)C=C1C(=O)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 35, 35, 105, 111, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 35, 105, 105, 111, 111] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036093 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036093 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036093/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036093 Building REAL250005036094 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036094' /scratch/stefan/7916117/working/building/REAL250005036094 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036094 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036094/0 /scratch/stefan/7916117/working/building/REAL250005036094 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/678 `/scratch/stefan/7916117/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1CC(CC(=O)NCCC2=NC(=O)O[N-]2)CCO1) `REAL250005036094.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036094 none CC(C)C1CC(CC(=O)NCCC2=NC(=O)O[N-]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 128, 201, 128, 128, 97, 35, 35, 35, 14, 7, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 201, 201, 201, 201, 201, 201, 201, 128, 128, 128, 128, 97, 97, 35, 14, 14, 7, 7, 128, 128, 128, 128] 201 rigid atoms, others: [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, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 941 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036094 none CC(C)C1CC(CC(=O)NCCC2=NC(=O)O[N-]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 5, 23, 23, 23, 63, 64, 128, 128, 128, 128, 128, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 23, 63, 63, 64, 64, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 41, 42, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036094 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036094 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036094/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036094 Building REAL250005036095 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036095' /scratch/stefan/7916117/working/building/REAL250005036095 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036095 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036095/0 /scratch/stefan/7916117/working/building/REAL250005036095 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/679 `/scratch/stefan/7916117/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036095.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036095 none COC1=NOC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 171, 171, 171, 171, 91, 91, 91, 22, 8, 1, 1, 1, 1, 1, 1, 1, 171, 199, 199, 199, 90, 22, 22, 8, 8, 171] 199 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036095 none COC1=NOC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 60, 84, 171, 171, 171, 171, 171, 1, 2, 2, 2, 12, 60, 60, 84, 84, 1] 199 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036095 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036095 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036095/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036095 Building REAL250005036096 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036096' /scratch/stefan/7916117/working/building/REAL250005036096 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036096 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036096/0 /scratch/stefan/7916117/working/building/REAL250005036096 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/680 `/scratch/stefan/7916117/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CO1) `REAL250005036096.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036096 none CCOC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 186, 130, 130, 130, 93, 93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 201, 201, 201, 201, 201, 92, 24, 24, 8, 8, 131] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 546 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036096 none CCOC1=NC(C(=O)NCCC2=NC(=O)O[N-]2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [28, 8, 1, 1, 1, 1, 1, 6, 6, 6, 22, 36, 130, 130, 130, 131, 131, 1, 1, 28, 28, 28, 28, 28, 6, 22, 22, 36, 36, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 17, 18, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036096 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036096 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036096/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036096 Building REAL250005036097 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036097' /scratch/stefan/7916117/working/building/REAL250005036097 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036097 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036097/0 /scratch/stefan/7916117/working/building/REAL250005036097 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/681 `/scratch/stefan/7916117/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN=C(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036097.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036097 none CCC1=NN=C(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 177, 177, 177, 177, 177, 177, 177, 62, 62, 62, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 177, 177, 177, 177, 62, 17, 17, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 499 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036097 none CCC1=NN=C(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 59, 63, 177, 177, 177, 177, 177, 6, 6, 6, 6, 6, 2, 2, 2, 1, 10, 59, 59, 63, 63] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036097 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036097 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036097/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036097 Building REAL250005036098 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036098' /scratch/stefan/7916117/working/building/REAL250005036098 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036098 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036098/0 /scratch/stefan/7916117/working/building/REAL250005036098 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/682 `/scratch/stefan/7916117/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N=N1) `REAL250005036098.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036098 none CCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 152, 152, 152, 56, 56, 56, 17, 8, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 201, 201, 201, 201, 201, 152, 56, 17, 17, 8, 8, 152, 152, 152] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 612 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036098 none CCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [7, 1, 1, 1, 1, 1, 10, 10, 10, 51, 58, 152, 152, 152, 152, 152, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 10, 51, 51, 58, 58, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 19, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036098 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036098 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036098/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036098 Building REAL250005036099 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036099' /scratch/stefan/7916117/working/building/REAL250005036099 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036099 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036099/0 /scratch/stefan/7916117/working/building/REAL250005036099 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/683 `/scratch/stefan/7916117/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CO1) `REAL250005036099.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036099 none NC(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CO1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 201, 134, 134, 66, 66, 66, 22, 8, 1, 1, 1, 1, 1, 1, 1, 134, 134, 201, 201, 134, 66, 22, 22, 8, 8, 134] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 579 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036099 none NC(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CO1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 6, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 5, 5, 5, 33, 58, 134, 134, 134, 134, 134, 1, 1, 5, 5, 1, 5, 33, 33, 58, 58, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 21, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036099 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036099 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036099/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036099 Building REAL250005036100 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036100' /scratch/stefan/7916117/working/building/REAL250005036100 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036100 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036100/0 /scratch/stefan/7916117/working/building/REAL250005036100 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/684 `/scratch/stefan/7916117/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1CC2(C1)CC(C(=O)NCCC1=NC(=O)O[N-]1)C2) `REAL250005036100.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036100 none N#CC1CC2(C1)CC(C(=O)NCCC1=NC(=O)O[N-]1)C2 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 160, 160, 160, 160, 86, 86, 86, 23, 8, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 160, 160, 160, 160, 160, 85, 23, 23, 8, 8, 160, 160] 160 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 497 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: REAL250005036100 none N#CC1CC2(C1)CC(C(=O)NCCC1=NC(=O)O[N-]1)C2 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 63, 96, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 63, 63, 96, 96, 1, 1] 160 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 508 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036100 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036100 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036100/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036100 Building REAL250005036101 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036101' /scratch/stefan/7916117/working/building/REAL250005036101 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036101 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036101/0 /scratch/stefan/7916117/working/building/REAL250005036101 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/685 `/scratch/stefan/7916117/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC(CC(=O)NCCC2=NC(=O)O[N-]2)CCO1) `REAL250005036101.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036101 none CCC1CC(CC(=O)NCCC2=NC(=O)O[N-]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 176, 176, 176, 141, 53, 53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 176, 176, 176, 201, 201, 201, 201, 201, 176, 176, 176, 176, 141, 141, 53, 17, 17, 8, 8, 176, 176, 176, 176] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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: REAL250005036101 none CCC1CC(CC(=O)NCCC2=NC(=O)O[N-]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 26, 26, 83, 85, 176, 176, 176, 176, 176, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 6, 26, 83, 83, 85, 85, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 17, 18, 19, 25, 26, 27, 28, 37, 36] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036101 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036101 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036101/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036101 Building REAL250005036102 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036102' /scratch/stefan/7916117/working/building/REAL250005036102 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036102 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036102/0 /scratch/stefan/7916117/working/building/REAL250005036102 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/686 `/scratch/stefan/7916117/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCCC1) `REAL250005036102.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036102 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 22, 8, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 22, 22, 8, 8, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51] 51 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 183 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036102 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 9, 19, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 9, 9, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 51 rigid atoms, others: [0, 1, 2, 34, 36, 33, 38, 32, 37, 13, 14, 15, 16, 17, 18, 35, 27, 28, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036102 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036102 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036102/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036102 Building REAL250005036103 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036103' /scratch/stefan/7916117/working/building/REAL250005036103 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036103 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036103/0 /scratch/stefan/7916117/working/building/REAL250005036103 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/687 `/scratch/stefan/7916117/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NC(Cl)=C1) `REAL250005036103.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036103 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 1, 16, 1, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 47, 73, 181, 181, 181, 181, 181, 1, 1, 1, 1, 1, 1, 1, 1, 7, 47, 47, 73, 73, 1, 1, 1] 181 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 461 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036103 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 1, 16, 1, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 20, 8, 1, 1, 1, 1, 1, 1, 1, 73, 181, 181, 181, 181, 181, 181, 181, 73, 20, 20, 8, 8, 181, 181, 181] 181 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036103 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036103 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036103/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036103 Building REAL250005036104 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036104' /scratch/stefan/7916117/working/building/REAL250005036104 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036104 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036104/0 /scratch/stefan/7916117/working/building/REAL250005036104 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/688 `/scratch/stefan/7916117/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C) `REAL250005036104.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036104 none CCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 5, 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, 4, 7, 7, 7, 7, 7, 5, 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, 118, 118, 118, 75, 75, 75, 24, 8, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 201, 201, 201, 201, 201, 118, 74, 24, 24, 8, 8, 118, 118, 118] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 802 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036104 none CCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 5, 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, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 11, 11, 11, 43, 54, 118, 118, 118, 118, 118, 1, 1, 1, 6, 6, 6, 6, 6, 1, 11, 43, 43, 54, 54, 2, 2, 2] 201 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 24] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036104 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036104 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036104/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036104 Building REAL250005036105 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036105' /scratch/stefan/7916117/working/building/REAL250005036105 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036105 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036105/0 /scratch/stefan/7916117/working/building/REAL250005036105 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/689 `/scratch/stefan/7916117/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=NC=CN=C2N=C1) `REAL250005036105.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036105 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=NC=CN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 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: [7, 1, 7, 7, 38, 66, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 38, 38, 66, 66, 1, 1, 1, 1] 130 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 391 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036105 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=NC=CN=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 8, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 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: [59, 59, 23, 8, 1, 1, 1, 1, 1, 1, 1, 59, 130, 130, 130, 130, 130, 130, 130, 130, 130, 58, 23, 23, 8, 8, 130, 130, 130, 130] 130 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036105 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036105 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036105/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036105 Building REAL250005036106 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036106' /scratch/stefan/7916117/working/building/REAL250005036106 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036106 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036106/0 /scratch/stefan/7916117/working/building/REAL250005036106 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/690 `/scratch/stefan/7916117/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCOC1) `REAL250005036106.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036106 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 100, 100, 100, 24, 8, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 148, 148, 148, 148, 100, 25, 25, 8, 8, 148, 148, 148, 148, 148, 148, 148, 148] 148 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036106 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 5, 5, 31, 54, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 2, 2, 2, 5, 31, 31, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1] 148 rigid atoms, others: [0, 1, 2, 33, 32, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036106 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036106 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036106/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036106 Building REAL250005036107 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036107' /scratch/stefan/7916117/working/building/REAL250005036107 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036107 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036107/0 /scratch/stefan/7916117/working/building/REAL250005036107 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/691 `/scratch/stefan/7916117/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036107.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036107 none C#CCCCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 116, 141, 116, 110, 31, 31, 31, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 191, 191, 141, 141, 141, 141, 141, 141, 110, 110, 31, 15, 15, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 1183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036107 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036107 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036107/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036107 Building REAL250005036108 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036108' /scratch/stefan/7916117/working/building/REAL250005036108 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036108 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036108/0 /scratch/stefan/7916117/working/building/REAL250005036108 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/692 `/scratch/stefan/7916117/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C)CC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005036108.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036108 none CC1CC(C)CC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 90, 90, 90, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 24, 24, 8, 8, 201, 201] 201 rigid atoms, others: [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, 36, 37, 38]) total number of confs: 635 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036108 none CC1CC(C)CC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 57, 82, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 12, 57, 57, 82, 82, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 18, 19, 20, 21, 22, 23, 24, 25, 37, 29, 30, 31] set([32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036108 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036108 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036108/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036108 Building REAL250005036109 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036109' /scratch/stefan/7916117/working/building/REAL250005036109 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036109 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036109/0 /scratch/stefan/7916117/working/building/REAL250005036109 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/693 `/scratch/stefan/7916117/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=N1)OCCC2) `REAL250005036109.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036109 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=N1)OCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 61, 78, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 60, 60, 79, 79, 1, 1, 1, 1, 1, 1, 1, 1] 143 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036109 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=N1)OCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 12, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [71, 71, 20, 8, 1, 1, 1, 1, 1, 1, 1, 71, 143, 143, 143, 143, 143, 143, 143, 143, 143, 70, 20, 20, 8, 8, 143, 143, 143, 143, 143, 143, 143, 143] 143 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036109 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036109 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036109/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036109 Building REAL250005036110 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036110' /scratch/stefan/7916117/working/building/REAL250005036110 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036110 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036110/0 /scratch/stefan/7916117/working/building/REAL250005036110 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/694 `/scratch/stefan/7916117/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005036110.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036110 none CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 100, 100, 100, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 21, 21, 8, 8, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 601 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: REAL250005036110 none CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 13, 13, 13, 70, 101, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 13, 70, 70, 101, 101, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 17, 35, 24, 25, 26, 27, 28] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 29, 30, 31]) total number of confs: 585 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036110 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036110 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036110/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036110 Building REAL250005036111 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036111' /scratch/stefan/7916117/working/building/REAL250005036111 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036111 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036111/0 /scratch/stefan/7916117/working/building/REAL250005036111 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/695 `/scratch/stefan/7916117/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005036111.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036111 none CCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 193, 89, 89, 89, 43, 43, 43, 15, 7, 1, 1, 1, 1, 1, 1, 1, 89, 89, 201, 201, 201, 201, 201, 193, 193, 89, 43, 15, 15, 7, 7, 89] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036111 none CCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 1, 1, 1, 1, 1, 5, 5, 5, 23, 25, 89, 89, 89, 89, 89, 1, 1, 16, 16, 16, 16, 16, 8, 8, 1, 5, 23, 23, 25, 25, 1] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 17, 18, 26] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036111 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036111 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036111/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036111 Building REAL250005036112 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036112' /scratch/stefan/7916117/working/building/REAL250005036112 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036112 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036112/0 /scratch/stefan/7916117/working/building/REAL250005036112 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/696 `/scratch/stefan/7916117/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005036112.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036112 none C[C@H](C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 22, 22, 22, 78, 92, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 4, 4, 4, 22, 78, 78, 92, 92, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 531 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036112 none C[C@H](C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [168, 67, 168, 67, 67, 20, 8, 1, 1, 1, 1, 1, 1, 1, 168, 201, 201, 168, 201, 201, 168, 168, 168, 67, 20, 20, 8, 8, 201, 201, 168, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036112 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036112 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036112/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036112 Building REAL250005036113 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036113' /scratch/stefan/7916117/working/building/REAL250005036113 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036113 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036113/0 /scratch/stefan/7916117/working/building/REAL250005036113 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/697 `/scratch/stefan/7916117/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005036113.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036113 none C[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 22, 22, 22, 80, 93, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 4, 4, 4, 22, 80, 80, 93, 93, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 533 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036113 none C[C@@H](C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [169, 66, 169, 66, 66, 20, 8, 1, 1, 1, 1, 1, 1, 1, 169, 201, 201, 169, 201, 201, 169, 169, 169, 66, 20, 20, 8, 8, 201, 201, 169, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 787 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036113 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036113 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036113/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036113 Building REAL250005036114 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036114' /scratch/stefan/7916117/working/building/REAL250005036114 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036114 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036114/0 /scratch/stefan/7916117/working/building/REAL250005036114 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/698 `/scratch/stefan/7916117/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CC(C(=O)NCCC2=NC(=O)O[N-]2)CCO1) `REAL250005036114.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036114 none CCC1CC(C(=O)NCCC2=NC(=O)O[N-]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 120, 120, 120, 66, 66, 66, 20, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 201, 201, 201, 201, 201, 120, 120, 120, 120, 66, 20, 20, 8, 8, 120, 120, 120, 120] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 814 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036114 none CCC1CC(C(=O)NCCC2=NC(=O)O[N-]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [4, 1, 1, 1, 1, 1, 6, 6, 6, 30, 43, 120, 120, 120, 120, 120, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 30, 30, 43, 43, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 34, 16, 17, 18, 35, 24, 25, 26, 27, 36] set([0, 32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 28, 29, 30, 31]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036114 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036114 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036114/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036114 Building REAL250005036115 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036115' /scratch/stefan/7916117/working/building/REAL250005036115 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036115 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036115/0 /scratch/stefan/7916117/working/building/REAL250005036115 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/699 `/scratch/stefan/7916117/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005036115.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036115 none CC(C)CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 186, 201, 114, 114, 114, 54, 54, 54, 19, 8, 1, 1, 1, 1, 1, 1, 1, 114, 114, 201, 201, 201, 201, 201, 201, 201, 186, 186, 114, 54, 19, 19, 8, 8, 114] 201 rigid atoms, others: [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]) total number of confs: 761 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036115 none CC(C)CN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [7, 5, 7, 1, 1, 1, 1, 1, 5, 5, 5, 29, 38, 114, 114, 114, 114, 114, 1, 1, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 5, 29, 29, 38, 38, 1] 201 rigid atoms, others: [35, 3, 4, 5, 6, 7, 18, 19, 29] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036115 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036115 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036115/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036115 Building REAL250005036116 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036116' /scratch/stefan/7916117/working/building/REAL250005036116 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036116 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036116/0 /scratch/stefan/7916117/working/building/REAL250005036116 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/700 `/scratch/stefan/7916117/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036116.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036116 none CC(C)OCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 142, 201, 126, 105, 119, 42, 42, 42, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 115, 116, 126, 126, 119, 119, 42, 20, 20, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 983 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036116 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036116 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036116/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036116 Building REAL250005036117 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036117' /scratch/stefan/7916117/working/building/REAL250005036117 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036117 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036117/0 /scratch/stefan/7916117/working/building/REAL250005036117 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/701 `/scratch/stefan/7916117/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)(C)C)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036117.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036117 none CC1=NN(C(C)(C)C)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [132, 132, 132, 126, 132, 201, 201, 201, 132, 71, 71, 71, 24, 8, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 70, 25, 25, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 773 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: REAL250005036117 none CC1=NN(C(C)(C)C)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 4, 4, 4, 1, 1, 1, 12, 12, 12, 54, 68, 132, 132, 132, 132, 132, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 12, 54, 54, 68, 68] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 8, 9, 10] set([5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 390 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036117 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036117 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036117/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036117 Building REAL250005036118 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036118' /scratch/stefan/7916117/working/building/REAL250005036118 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036118 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036118/0 /scratch/stefan/7916117/working/building/REAL250005036118 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/702 `/scratch/stefan/7916117/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005036118.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036118 none CC(C)OC1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 118, 118, 117, 117, 89, 89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 201, 201, 201, 117, 88, 25, 25, 8, 8, 118] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 477 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036118 none CC(C)OC1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 10, 24, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 31, 117, 117, 117, 117, 117, 1, 1, 24, 24, 24, 24, 24, 24, 24, 1, 3, 19, 19, 31, 31, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 19, 20, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036118 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036118 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036118/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036118 Building REAL250005036119 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036119' /scratch/stefan/7916117/working/building/REAL250005036119 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036119 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036119/0 /scratch/stefan/7916117/working/building/REAL250005036119 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/703 `/scratch/stefan/7916117/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C=C1[O-]) `REAL250005036119.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036119 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 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: [4, 1, 4, 4, 8, 8, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 4, 8, 8, 8, 8, 1, 1, 1] 25 rigid atoms, others: [1, 11, 12, 13, 14, 15, 18, 19, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 21, 22, 23, 24, 25]) 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: REAL250005036119 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 5, 5, 4, 4, 25, 25, 25] 25 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036119 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036119 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036119/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036119 Building REAL250005036120 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036120' /scratch/stefan/7916117/working/building/REAL250005036120 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036120 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036120/0 /scratch/stefan/7916117/working/building/REAL250005036120 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/704 `/scratch/stefan/7916117/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCCS1(=O)=O) `REAL250005036120.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036120 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 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, 13, 67, 90, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 1, 1, 13, 67, 67, 90, 90, 1, 1, 1, 1, 1, 1, 1, 1, 1] 178 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 500 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036120 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCCS1(=O)=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 14, 11, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 24, 8, 1, 1, 1, 1, 1, 1, 1, 100, 178, 178, 178, 178, 178, 178, 178, 100, 24, 24, 8, 8, 178, 178, 178, 178, 178, 178, 178, 178, 178] 178 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 559 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036120 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036120 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036120/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036120 Building REAL250005036121 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036121' /scratch/stefan/7916117/working/building/REAL250005036121 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036121 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036121/0 /scratch/stefan/7916117/working/building/REAL250005036121 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/705 `/scratch/stefan/7916117/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=N1) `REAL250005036121.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036121 none COCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 193, 96, 85, 96, 53, 53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 201, 201, 201, 201, 201, 193, 193, 96, 53, 17, 17, 8, 8, 96, 96, 96] 201 rigid atoms, others: [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, 36]) total number of confs: 823 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036121 none COCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [32, 10, 8, 1, 1, 1, 1, 1, 3, 3, 3, 21, 23, 96, 96, 96, 96, 96, 1, 1, 1, 32, 32, 32, 10, 10, 8, 8, 1, 3, 21, 21, 23, 23, 2, 2, 2] 201 rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 20, 28] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036121 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036121 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036121/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036121 Building REAL250005036122 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036122' /scratch/stefan/7916117/working/building/REAL250005036122 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036122 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036122/0 /scratch/stefan/7916117/working/building/REAL250005036122 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/706 `/scratch/stefan/7916117/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036122.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036122 none CN1C(=O)CC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 168, 168, 104, 168, 104, 104, 24, 8, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 168, 168, 168, 104, 24, 24, 8, 8] 168 rigid atoms, others: [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]) total number of confs: 525 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: REAL250005036122 none CN1C(=O)CC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 55, 77, 168, 168, 168, 168, 168, 1, 1, 1, 1, 1, 1, 1, 11, 55, 55, 77, 77] 168 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30]) total number of confs: 460 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036122 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036122 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036122/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036122 Building REAL250005036123 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036123' /scratch/stefan/7916117/working/building/REAL250005036123 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005036123 as failed and skipping /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `/scratch/stefan/7916117/failed' `/scratch/stefan/7916117/working/building/REAL250005036123' -> `/scratch/stefan/7916117/failed/REAL250005036123' Building REAL250005036124 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036124' /scratch/stefan/7916117/working/building/REAL250005036124 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036124 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036124/0 /scratch/stefan/7916117/working/building/REAL250005036124 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/707 `/scratch/stefan/7916117/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(O)=CC=C1Cl) `REAL250005036124.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036124 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(O)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 296 conformations in input total number of sets (complete confs): 296 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 42, 67, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 1, 1, 1, 7, 42, 42, 67, 67, 1, 2, 1, 1] 296 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 25]) total number of confs: 405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036124 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(O)=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 296 conformations in input total number of sets (complete confs): 296 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 22, 8, 1, 1, 1, 1, 1, 1, 1, 87, 148, 148, 148, 148, 148, 148, 148, 87, 22, 22, 8, 8, 148, 296, 148, 148] 296 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 660 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036124 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036124 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036124/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036124 Building REAL250005036125 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036125' /scratch/stefan/7916117/working/building/REAL250005036125 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036125 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036125/0 /scratch/stefan/7916117/working/building/REAL250005036125 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/708 `/scratch/stefan/7916117/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1) `REAL250005036125.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036125 none C=CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 141, 51, 51, 51, 17, 8, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 201, 201, 201, 201, 201, 51, 17, 17, 8, 8, 141, 141, 141, 141, 141, 141] 201 rigid atoms, others: [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, 33]) total number of confs: 755 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036125 none C=CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [16, 5, 1, 1, 1, 6, 6, 6, 33, 37, 141, 141, 141, 141, 141, 1, 1, 1, 16, 16, 16, 5, 5, 6, 33, 33, 37, 37, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036125 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036125 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036125/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036125 Building REAL250005036126 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036126' /scratch/stefan/7916117/working/building/REAL250005036126 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036126 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036126/0 /scratch/stefan/7916117/working/building/REAL250005036126 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/709 `/scratch/stefan/7916117/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C12CC(C3=CC=CC=C3)(C1)C2) `REAL250005036126.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036126 none O=C(NCCC1=NC(=O)O[N-]1)C12CC(C3=CC=CC=C3)(C1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 45, 69, 127, 127, 127, 127, 127, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 6, 45, 45, 69, 69, 1, 1, 7, 7, 1, 7, 7, 1, 1, 1, 1] 131 rigid atoms, others: [1, 34, 35, 36, 37, 11, 12, 13, 14, 20, 21, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) 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: REAL250005036126 none O=C(NCCC1=NC(=O)O[N-]1)C12CC(C3=CC=CC=C3)(C1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [70, 70, 24, 8, 1, 1, 1, 1, 1, 1, 1, 70, 123, 123, 123, 124, 124, 124, 124, 124, 123, 123, 69, 25, 25, 8, 8, 123, 123, 124, 124, 124, 124, 124, 123, 123, 123, 123] 124 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036126 none O=C(NCCC1=NC(=O)O[N-]1)C12CC(C3=CC=CC=C3)(C1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 7, 24, 24, 78, 87, 131, 131, 131, 131, 131, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 24, 78, 78, 87, 87, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7] 131 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37]) total number of confs: 400 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036126 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036126 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036126/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036126 Building REAL250005036127 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036127' /scratch/stefan/7916117/working/building/REAL250005036127 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036127 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036127/0 /scratch/stefan/7916117/working/building/REAL250005036127 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/710 `/scratch/stefan/7916117/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN2CCCOC2=C1) `REAL250005036127.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036127 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN2CCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 56, 76, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 56, 56, 76, 76, 1, 1, 1, 1, 1, 1, 1] 114 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 375 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036127 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN2CCCOC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 5, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 22, 8, 1, 1, 1, 1, 1, 1, 1, 63, 114, 114, 114, 114, 114, 114, 114, 114, 63, 22, 22, 8, 8, 114, 114, 114, 114, 114, 114, 114] 114 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036127 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036127 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036127/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036127 Building REAL250005036128 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036128' /scratch/stefan/7916117/working/building/REAL250005036128 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036128 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036128/0 /scratch/stefan/7916117/working/building/REAL250005036128 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/711 `/scratch/stefan/7916117/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC2=CC=CC=C2C1) `REAL250005036128.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036128 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 56, 90, 182, 182, 182, 182, 182, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 56, 56, 90, 90, 1, 1, 1, 1, 1, 1, 1, 1, 1] 182 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 527 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036128 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2=CC=CC=C2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [89, 89, 20, 8, 1, 1, 1, 1, 1, 1, 1, 89, 182, 182, 182, 182, 182, 182, 182, 182, 88, 20, 20, 8, 8, 182, 182, 182, 182, 182, 182, 182, 182, 182] 182 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 554 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036128 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036128 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036128/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036128 Building REAL250005036129 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036129' /scratch/stefan/7916117/working/building/REAL250005036129 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036129 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036129/0 /scratch/stefan/7916117/working/building/REAL250005036129 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/712 `/scratch/stefan/7916117/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(CC(=O)NCCC2=NC(=O)O[N-]2)CCC1) `REAL250005036129.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036129 none COC1(CC(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 167, 61, 61, 61, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 167, 167, 61, 19, 19, 8, 8, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 33]) 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: REAL250005036129 none COC1(CC(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 1, 1, 1, 9, 32, 32, 32, 110, 118, 201, 201, 201, 201, 201, 1, 1, 1, 5, 5, 5, 9, 9, 32, 110, 110, 118, 118, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 33, 15, 16, 17, 28, 29, 30, 31] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036129 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036129 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036129/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036129 Building REAL250005036130 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036130' /scratch/stefan/7916117/working/building/REAL250005036130 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036130 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036130/0 /scratch/stefan/7916117/working/building/REAL250005036130 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/713 `/scratch/stefan/7916117/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OCCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036130.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036130 none CC1OCCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 135, 135, 135, 82, 82, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 81, 25, 25, 8, 8] 135 rigid atoms, others: [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]) total number of confs: 456 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036130 none CC1OCCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 65, 135, 135, 135, 135, 135, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 9, 45, 45, 65, 65] 135 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036130 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036130 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036130/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036130 Building REAL250005036131 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036131' /scratch/stefan/7916117/working/building/REAL250005036131 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036131 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036131/0 /scratch/stefan/7916117/working/building/REAL250005036131 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/714 `/scratch/stefan/7916117/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C([N+](=O)[O-])C(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005036131.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036131 none CCN1C=C([N+](=O)[O-])C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 11, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 140, 140, 140, 140, 140, 140, 140, 56, 56, 56, 20, 8, 1, 1, 1, 1, 1, 1, 1, 140, 201, 201, 201, 201, 201, 140, 56, 20, 20, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 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: REAL250005036131 none CCN1C=C([N+](=O)[O-])C(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 11, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 50, 140, 140, 140, 140, 140, 1, 8, 8, 8, 8, 8, 1, 9, 43, 43, 50, 50] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 26] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036131 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036131 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036131/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036131 Building REAL250005036132 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036132' /scratch/stefan/7916117/working/building/REAL250005036132 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036132 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036132/0 /scratch/stefan/7916117/working/building/REAL250005036132 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/715 `/scratch/stefan/7916117/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl) `REAL250005036132.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036132 none CC1=CSC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 183, 183, 81, 81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 183, 183, 183, 183, 183, 183, 81, 25, 25, 8, 8] 183 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036132 none CC1=CSC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 73, 183, 183, 183, 183, 183, 1, 1, 2, 2, 2, 1, 7, 39, 39, 73, 73] 183 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 21] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036132 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036132 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036132/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036132 Building REAL250005036133 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036133' /scratch/stefan/7916117/working/building/REAL250005036133 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036133 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036133/0 /scratch/stefan/7916117/working/building/REAL250005036133 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/716 `/scratch/stefan/7916117/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1CCOCC1) `REAL250005036133.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036133 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 6, 21, 21, 78, 84, 201, 201, 201, 201, 201, 1, 6, 6, 1, 1, 1, 1, 1, 1, 21, 78, 78, 84, 84, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 11, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24]) total number of confs: 509 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036133 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 19, 8, 1, 1, 1, 1, 1, 1, 1, 70, 166, 166, 166, 201, 201, 201, 201, 199, 70, 19, 19, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 816 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036133 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036133 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036133/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036133 Building REAL250005036134 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036134' /scratch/stefan/7916117/working/building/REAL250005036134 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036134 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036134/0 /scratch/stefan/7916117/working/building/REAL250005036134 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/717 `/scratch/stefan/7916117/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2CCC2)C=C1) `REAL250005036134.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036134 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 17, 32, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 8, 8, 8, 1, 1, 4, 17, 17, 32, 32, 1, 1, 8, 9, 8, 8, 9, 8, 9, 1, 1] 201 rigid atoms, others: [1, 35, 36, 11, 12, 13, 14, 15, 19, 20, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 242 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: REAL250005036134 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 58, 24, 8, 1, 1, 1, 1, 1, 1, 1, 58, 89, 89, 58, 58, 201, 201, 201, 89, 89, 58, 24, 24, 8, 8, 89, 89, 201, 201, 201, 201, 201, 201, 201, 89, 89] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 723 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: REAL250005036134 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C2CCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 19, 19, 80, 117, 201, 201, 201, 201, 201, 4, 8, 8, 1, 1, 1, 1, 1, 8, 8, 19, 80, 80, 117, 117, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9] 201 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36]) total number of confs: 666 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036134 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036134 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036134/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036134 Building REAL250005036135 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036135' /scratch/stefan/7916117/working/building/REAL250005036135 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036135 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036135/0 /scratch/stefan/7916117/working/building/REAL250005036135 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/718 `/scratch/stefan/7916117/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=NC=CS1) `REAL250005036135.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036135 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=NC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [61, 13, 61, 61, 140, 140, 201, 201, 201, 201, 201, 1, 13, 13, 1, 1, 1, 1, 1, 61, 140, 140, 140, 140, 1, 1] 201 rigid atoms, others: [11, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 19, 20, 21, 22, 23]) 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: REAL250005036135 none O=C(NCCC1=NC(=O)O[N-]1)C(F)(F)C1=NC=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 18, 8, 1, 1, 1, 1, 1, 1, 1, 40, 137, 137, 137, 201, 201, 201, 201, 40, 18, 18, 8, 8, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036135 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036135 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036135/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036135 Building REAL250005036136 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036136' /scratch/stefan/7916117/working/building/REAL250005036136 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036136 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036136/0 /scratch/stefan/7916117/working/building/REAL250005036136 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/719 `/scratch/stefan/7916117/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CS1) `REAL250005036136.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036136 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 68, 102, 168, 168, 168, 168, 168, 1, 1, 1, 1, 1, 1, 13, 68, 68, 102, 102, 1, 1] 168 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036136 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(Cl)=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 24, 8, 1, 1, 1, 1, 1, 1, 1, 79, 168, 168, 168, 168, 168, 79, 24, 24, 8, 8, 168, 168] 168 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036136 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036136 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036136/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036136 Building REAL250005036137 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036137' /scratch/stefan/7916117/working/building/REAL250005036137 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036137 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036137/0 /scratch/stefan/7916117/working/building/REAL250005036137 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/720 `/scratch/stefan/7916117/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=NC=N1)NCCC1=NC(=O)O[N-]1) `REAL250005036137.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036137 none O=C(CCC1=CC=NC=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 5, 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: [39, 39, 39, 127, 159, 201, 201, 201, 201, 201, 17, 7, 1, 1, 1, 1, 1, 1, 1, 127, 127, 159, 159, 201, 201, 201, 39, 17, 17, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 761 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036137 none O=C(CCC1=CC=NC=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 5, 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: [47, 10, 6, 1, 1, 1, 1, 1, 1, 1, 47, 47, 126, 129, 201, 201, 201, 201, 201, 10, 10, 6, 6, 1, 1, 1, 47, 128, 128, 131, 131] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24, 25] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 641 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036137 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036137 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036137/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036137 Building REAL250005036138 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036138' /scratch/stefan/7916117/working/building/REAL250005036138 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036138 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036138/0 /scratch/stefan/7916117/working/building/REAL250005036138 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/721 `/scratch/stefan/7916117/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C(Cl)S1) `REAL250005036138.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036138 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 108, 108, 108, 20, 8, 1, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 199, 199, 199, 107, 20, 20, 8, 8] 199 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 454 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036138 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C(Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 10, 59, 91, 199, 199, 199, 199, 199, 1, 1, 1, 1, 2, 2, 2, 10, 59, 59, 91, 91] 199 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036138 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036138 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036138/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036138 Building REAL250005036139 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036139' /scratch/stefan/7916117/working/building/REAL250005036139 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036139 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036139/0 /scratch/stefan/7916117/working/building/REAL250005036139 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/722 `/scratch/stefan/7916117/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=CN=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036139.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036139 none CCCOC1=CC=CN=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 197, 171, 92, 92, 92, 92, 91, 91, 43, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 92, 92, 91, 42, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 505 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036139 none CCCOC1=CC=CN=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [41, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 91, 91, 91, 91, 91, 45, 45, 45, 45, 45, 25, 25, 1, 1, 1, 5, 21, 21, 21, 21] 201 rigid atoms, others: [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, 34, 35]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036139 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036139 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036139/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036139 Building REAL250005036140 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036140' /scratch/stefan/7916117/working/building/REAL250005036140 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036140 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036140/0 /scratch/stefan/7916117/working/building/REAL250005036140 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/723 `/scratch/stefan/7916117/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C=CN=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=N1) `REAL250005036140.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036140 none CC1=CN2C=CN=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 39, 39, 39, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 39, 23, 23, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036140 none CC1=CN2C=CN=C(C(=O)NCCC3=NC(=O)O[N-]3)C2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 64, 98, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 12, 64, 64, 98, 98] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 581 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036140 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036140 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036140/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036140 Building REAL250005036141 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036141' /scratch/stefan/7916117/working/building/REAL250005036141 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036141 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036141/0 /scratch/stefan/7916117/working/building/REAL250005036141 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/724 `/scratch/stefan/7916117/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(O)=C1) `REAL250005036141.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036141 none CCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 110, 109, 110, 110, 65, 65, 65, 20, 8, 1, 1, 1, 1, 1, 1, 1, 110, 110, 110, 201, 201, 201, 201, 201, 110, 110, 65, 20, 20, 8, 8, 220, 110] 402 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1062 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: REAL250005036141 none CCC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(O)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 42, 51, 110, 110, 110, 110, 110, 1, 1, 1, 5, 5, 5, 4, 4, 1, 1, 9, 42, 42, 51, 51, 2, 1] 402 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 17, 18, 19, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 309 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036141 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036141 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036141/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036141 Building REAL250005036142 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036142' /scratch/stefan/7916117/working/building/REAL250005036142 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036142 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036142/0 /scratch/stefan/7916117/working/building/REAL250005036142 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/725 `/scratch/stefan/7916117/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1) `REAL250005036142.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036142 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 61, 61, 61, 24, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 105, 105, 61, 25, 24, 8, 8, 105, 105, 105, 105, 105, 105, 105, 105, 105, 105] 105 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL250005036142 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 18, 34, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 2, 2, 2, 2, 18, 18, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 105 rigid atoms, others: [0, 1, 2, 34, 33, 32, 13, 14, 15, 16, 17, 35, 26, 27, 28, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036142 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036142 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036142/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036142 Building REAL250005036143 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036143' /scratch/stefan/7916117/working/building/REAL250005036143 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036143 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036143/0 /scratch/stefan/7916117/working/building/REAL250005036143 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/726 `/scratch/stefan/7916117/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(Cl)=N1) `REAL250005036143.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036143 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 16, 8, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 60, 82, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 1, 12, 60, 60, 82, 82, 1, 1] 147 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) 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: REAL250005036143 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 16, 8, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 89, 147, 147, 147, 147, 147, 147, 89, 24, 24, 8, 8, 147, 147] 147 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036143 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036143 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036143/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036143 Building REAL250005036144 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036144' /scratch/stefan/7916117/working/building/REAL250005036144 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036144 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036144/0 /scratch/stefan/7916117/working/building/REAL250005036144 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/727 `/scratch/stefan/7916117/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1OCCCO1)NCCC1=NC(=O)O[N-]1) `REAL250005036144.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036144 none O=C(CC1OCCCO1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 182, 201, 201, 201, 201, 201, 20, 8, 1, 1, 1, 1, 1, 1, 1, 182, 182, 201, 201, 201, 201, 201, 201, 201, 72, 20, 20, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036144 none O=C(CC1OCCCO1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 12, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 5, 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: [27, 5, 1, 1, 1, 1, 1, 1, 1, 27, 27, 94, 107, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 27, 94, 94, 107, 107] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31]) total number of confs: 567 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036144 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036144 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036144/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036144 Building REAL250005036145 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036145' /scratch/stefan/7916117/working/building/REAL250005036145 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036145 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036145/0 /scratch/stefan/7916117/working/building/REAL250005036145 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/728 `/scratch/stefan/7916117/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(Cl)=C1) `REAL250005036145.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036145 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [7, 1, 7, 7, 39, 75, 152, 152, 152, 152, 152, 1, 1, 1, 1, 1, 1, 7, 39, 39, 75, 75, 1, 1] 152 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 460 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036145 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [67, 67, 24, 8, 1, 1, 1, 1, 1, 1, 1, 67, 152, 152, 152, 152, 152, 66, 24, 24, 8, 8, 152, 152] 152 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036145 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036145 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036145/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036145 Building REAL250005036146 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036146' /scratch/stefan/7916117/working/building/REAL250005036146 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036146 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036146/0 /scratch/stefan/7916117/working/building/REAL250005036146 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/729 `/scratch/stefan/7916117/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1) `REAL250005036146.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036146 none C#CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 120, 69, 69, 69, 20, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 120, 120, 201, 201, 201, 69, 21, 20, 8, 8, 120, 120, 120, 120, 120, 120, 120, 120, 120, 120] 201 rigid atoms, others: [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, 33, 34, 35, 36, 37]) total number of confs: 863 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036146 none C#CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 1, 1, 1, 2, 2, 2, 14, 26, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 9, 9, 9, 2, 14, 14, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 37, 35, 34, 15, 16, 17, 18, 19, 36, 28, 29, 30, 31] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036146 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036146 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036146/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036146 Building REAL250005036147 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036147' /scratch/stefan/7916117/working/building/REAL250005036147 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036147 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036147/0 /scratch/stefan/7916117/working/building/REAL250005036147 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/730 `/scratch/stefan/7916117/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005036147.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036147 none COC1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 164, 164, 164, 164, 84, 84, 84, 24, 8, 1, 1, 1, 1, 1, 1, 1, 164, 164, 201, 201, 201, 164, 164, 164, 164, 164, 164, 84, 25, 25, 8, 8, 164, 164, 164, 164] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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: REAL250005036147 none COC1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 27, 44, 164, 164, 164, 164, 164, 1, 1, 9, 9, 9, 1, 1, 1, 1, 1, 1, 4, 27, 27, 44, 44, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 34, 17, 18, 35, 22, 23, 24, 25, 26, 27, 36] set([0, 32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036147 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036147 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036147/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036147 Building REAL250005036148 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036148' /scratch/stefan/7916117/working/building/REAL250005036148 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036148 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036148/0 /scratch/stefan/7916117/working/building/REAL250005036148 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/731 `/scratch/stefan/7916117/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(=O)CCC(C(=O)NCCC2=NC(=O)O[N-]2)C1(C)C) `REAL250005036148.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036148 none CC1C(=O)CCC(C(=O)NCCC2=NC(=O)O[N-]2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 59, 59, 59, 21, 8, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 84, 59, 21, 21, 8, 8, 84, 84, 84, 84, 84, 84] 84 rigid atoms, others: [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, 36, 37, 38, 39, 40]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036148 none CC1C(=O)CCC(C(=O)NCCC2=NC(=O)O[N-]2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 6, 6, 6, 22, 35, 84, 84, 84, 84, 84, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 22, 22, 35, 35, 2, 2, 2, 2, 2, 2] 84 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036148 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036148 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036148/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036148 Building REAL250005036149 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036149' /scratch/stefan/7916117/working/building/REAL250005036149 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036149 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036149/0 /scratch/stefan/7916117/working/building/REAL250005036149 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/732 `/scratch/stefan/7916117/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CNC=C(F)C1=O) `REAL250005036149.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036149 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNC=C(F)C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 15, 1, 11, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 76, 113, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 13, 76, 76, 113, 113, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005036149 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNC=C(F)C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 15, 1, 11, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 24, 8, 1, 1, 1, 1, 1, 1, 1, 109, 201, 201, 201, 201, 201, 201, 201, 109, 25, 24, 8, 8, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036149 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036149 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036149/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036149 Building REAL250005036150 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036150' /scratch/stefan/7916117/working/building/REAL250005036150 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036150 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036150/0 /scratch/stefan/7916117/working/building/REAL250005036150 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/733 `/scratch/stefan/7916117/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005036150.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036150 none CCN1C=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 130, 130, 130, 101, 41, 41, 41, 17, 8, 1, 1, 1, 1, 1, 1, 1, 130, 130, 201, 201, 201, 201, 201, 130, 101, 101, 41, 17, 17, 8, 8, 130] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 882 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036150 none CCN1C=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 1, 1, 6, 13, 13, 13, 43, 47, 130, 130, 130, 130, 130, 1, 1, 6, 6, 6, 6, 6, 1, 6, 6, 13, 43, 43, 47, 47, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 17, 18, 24] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036150 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036150 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036150/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036150 Building REAL250005036151 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036151' /scratch/stefan/7916117/working/building/REAL250005036151 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036151 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036151/0 /scratch/stefan/7916117/working/building/REAL250005036151 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/734 `/scratch/stefan/7916117/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005036151.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036151 none CC(C)N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 168, 201, 168, 168, 68, 68, 68, 20, 8, 1, 1, 1, 1, 1, 1, 1, 168, 168, 201, 201, 201, 201, 201, 201, 201, 168, 67, 20, 20, 8, 8, 168] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 546 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036151 none CC(C)N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [13, 1, 13, 1, 1, 1, 1, 5, 5, 5, 29, 42, 168, 168, 168, 168, 168, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 5, 29, 29, 42, 42, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 17, 18, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036151 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036151 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036151/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036151 Building REAL250005036152 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036152' /scratch/stefan/7916117/working/building/REAL250005036152 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036152 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036152/0 /scratch/stefan/7916117/working/building/REAL250005036152 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/735 `/scratch/stefan/7916117/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005036152.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036152 none NC(=O)C1CCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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: [8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 153, 201, 153, 153, 153, 153, 57, 57, 57, 17, 8, 1, 1, 1, 1, 1, 1, 1, 153, 201, 201, 153, 153, 153, 153, 153, 153, 153, 153, 57, 17, 17, 8, 8, 153, 153] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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: REAL250005036152 none NC(=O)C1CCCC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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: [8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 9, 1, 1, 1, 1, 1, 1, 11, 11, 11, 53, 58, 153, 153, 153, 153, 153, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 11, 53, 53, 58, 58, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 36, 19, 22, 23, 24, 25, 26, 27, 28, 29, 35] set([0, 32, 2, 34, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 30, 31]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036152 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036152 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036152/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036152 Building REAL250005036153 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036153' /scratch/stefan/7916117/working/building/REAL250005036153 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036153 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036153/0 /scratch/stefan/7916117/working/building/REAL250005036153 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/736 `/scratch/stefan/7916117/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036153.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036153 none CCC1=CC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 178, 178, 178, 148, 178, 177, 116, 25, 25, 25, 13, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 178, 178, 178, 178, 116, 116, 25, 13, 13, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036153 none CCC1=CC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 31, 92, 92, 178, 178, 178, 178, 178, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 31, 92, 92, 92, 92] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 519 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036153 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036153 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036153/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036153 Building REAL250005036154 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036154' /scratch/stefan/7916117/working/building/REAL250005036154 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036154 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036154/0 /scratch/stefan/7916117/working/building/REAL250005036154 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/737 `/scratch/stefan/7916117/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NOC2=C1CCCCC2) `REAL250005036154.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036154 none O=C(NCCC1=NC(=O)O[N-]1)C1=NOC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 66, 98, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 66, 66, 98, 98, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 564 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: REAL250005036154 none O=C(NCCC1=NC(=O)O[N-]1)C1=NOC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 12, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 22, 8, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 22, 22, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 455 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036154 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036154 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036154/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036154 Building REAL250005036155 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036155' /scratch/stefan/7916117/working/building/REAL250005036155 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036155 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036155/0 /scratch/stefan/7916117/working/building/REAL250005036155 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/738 `/scratch/stefan/7916117/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)[C@@H]1C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C1(C)C) `REAL250005036155.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036155 none CC(=O)[C@@H]1C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 23, 25, 23, 23, 14, 9, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 23, 14, 14, 9, 9, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 100 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: REAL250005036155 none CC(=O)[C@@H]1C[C@H](C(=O)NCCC2=NC(=O)O[N-]2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 11, 25, 25, 25, 25, 25, 1, 1, 1, 4, 4, 4, 1, 1, 4, 10, 10, 11, 11, 2, 2, 2, 2, 2, 2] 25 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 20, 21, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036155 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036155 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036155/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036155 Building REAL250005036156 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036156' /scratch/stefan/7916117/working/building/REAL250005036156 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036156 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036156/0 /scratch/stefan/7916117/working/building/REAL250005036156 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/739 `/scratch/stefan/7916117/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036156.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036156 none COC1=CC(C)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 179, 179, 179, 149, 179, 179, 179, 64, 64, 64, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 179, 179, 179, 179, 179, 179, 64, 20, 20, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 535 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036156 none COC1=CC(C)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 1, 12, 12, 12, 63, 75, 179, 179, 179, 179, 179, 3, 3, 3, 1, 2, 2, 2, 1, 1, 12, 63, 63, 75, 75] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036156 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036156 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036156/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036156 Building REAL250005036157 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036157' /scratch/stefan/7916117/working/building/REAL250005036157 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036157 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036157/0 /scratch/stefan/7916117/working/building/REAL250005036157 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/740 `/scratch/stefan/7916117/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CC(C)(C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036157.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036157 none CC(=O)CC(C)(C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 187, 201, 135, 75, 135, 135, 37, 37, 37, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 187, 187, 135, 135, 135, 135, 135, 135, 75, 75, 37, 17, 17, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 952 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036157 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036157 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036157/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036157 Building REAL250005036158 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036158' /scratch/stefan/7916117/working/building/REAL250005036158 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036158 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036158/0 /scratch/stefan/7916117/working/building/REAL250005036158 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/741 `/scratch/stefan/7916117/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005036158.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036158 none CC(=O)N1CC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 187, 201, 187, 187, 71, 71, 71, 21, 8, 1, 1, 1, 1, 1, 1, 1, 187, 201, 201, 201, 187, 187, 187, 71, 21, 21, 8, 8, 187, 187] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL250005036158 none CC(=O)N1CC(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 11, 11, 11, 61, 88, 187, 187, 187, 187, 187, 1, 3, 3, 3, 1, 1, 1, 11, 61, 61, 88, 88, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 17, 21, 22, 23, 29, 30] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 24, 25, 26, 27, 28]) total number of confs: 507 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036158 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036158 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036158/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036158 Building REAL250005036159 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036159' /scratch/stefan/7916117/working/building/REAL250005036159 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036159 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036159/0 /scratch/stefan/7916117/working/building/REAL250005036159 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/742 `/scratch/stefan/7916117/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1O) `REAL250005036159.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036159 none N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1O NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 63, 63, 63, 22, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 62, 22, 22, 8, 8, 105, 210] 210 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 487 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036159 none N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1O NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 210 conformations in input total number of sets (complete confs): 210 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 55, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 7, 33, 33, 55, 55, 1, 2] 210 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 28]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036159 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036159/1 /scratch/stefan/7916117/working/building/REAL250005036159 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/743 `/scratch/stefan/7916117/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1[O-]) `REAL250005036159.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036159 none N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1[O-] NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 86, 53, 53, 53, 24, 8, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 52, 24, 24, 8, 8, 86] 86 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL250005036159 none N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1[O-] NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 34, 49, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 7, 34, 34, 49, 49, 1] 86 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036159 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036159 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036159/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036159/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036159 Building REAL250005036160 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036160' /scratch/stefan/7916117/working/building/REAL250005036160 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036160 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036160/0 /scratch/stefan/7916117/working/building/REAL250005036160 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/744 `/scratch/stefan/7916117/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1N=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036160.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036160 none COCCN1N=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 190, 190, 108, 108, 108, 108, 108, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 190, 190, 190, 190, 108, 108, 49, 17, 17, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036160 none COCCN1N=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 24, 27, 108, 108, 108, 108, 108, 16, 16, 16, 6, 6, 6, 6, 1, 1, 6, 24, 24, 27, 27] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036160 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036160 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036160/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036160 Building REAL250005036161 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036161' /scratch/stefan/7916117/working/building/REAL250005036161 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036161 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036161/0 /scratch/stefan/7916117/working/building/REAL250005036161 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/745 `/scratch/stefan/7916117/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCCN1CCOCC1)NCCC1=NC(=O)O[N-]1) `REAL250005036161.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036161 none O=C(CCCCN1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 10, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 113, 111, 128, 145, 201, 201, 201, 201, 201, 15, 7, 1, 1, 1, 1, 1, 1, 1, 113, 113, 128, 128, 128, 128, 145, 145, 201, 201, 201, 201, 201, 201, 201, 201, 40, 15, 15, 7, 7] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 822 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036161 none O=C(CCCCN1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 10, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 11, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 39, 39, 116, 118, 201, 201, 201, 201, 201, 11, 11, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 39, 116, 116, 118, 118] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036161 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036161/1 /scratch/stefan/7916117/working/building/REAL250005036161 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/746 `/scratch/stefan/7916117/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC[NH+]1CCOCC1)NCCC1=NC(=O)O[N-]1) `REAL250005036161.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036161 none O=C(CCCC[NH+]1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 66, 70, 76, 80, 99, 99, 99, 99, 99, 99, 17, 8, 1, 1, 1, 1, 1, 1, 1, 66, 66, 76, 76, 76, 76, 80, 80, 99, 99, 99, 99, 99, 99, 99, 99, 46, 17, 17, 8, 8] 99 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 470 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: REAL250005036161 none O=C(CCCC[NH+]1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 9, 6, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [30, 15, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 47, 47, 99, 99, 99, 99, 99, 15, 15, 7, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 30, 47, 47, 47, 47] 99 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 37, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42]) total number of confs: 289 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036161 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036161 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036161/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036161/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036161 Building REAL250005036162 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036162' /scratch/stefan/7916117/working/building/REAL250005036162 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036162 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036162/0 /scratch/stefan/7916117/working/building/REAL250005036162 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/747 `/scratch/stefan/7916117/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(O)=C1O) `REAL250005036162.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036162/0/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: REAL250005036162 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(O)=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 12, 1, 12, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 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: [9, 1, 9, 9, 30, 35, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 30, 30, 35, 35, 1, 1, 2, 2] 268 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 27, 28]) total number of confs: 188 number of broken/clashed sets: 95 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036162 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(O)=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 12, 1, 12, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 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: [49, 49, 19, 8, 1, 1, 1, 1, 1, 1, 1, 49, 67, 67, 67, 67, 67, 67, 67, 67, 49, 19, 19, 8, 8, 67, 67, 134, 134] 268 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 473 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036162 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036162/1 /scratch/stefan/7916117/working/building/REAL250005036162 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/748 `/scratch/stefan/7916117/working/3D/748' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(O)=C1[O-]) `REAL250005036162.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036162 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(O)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 12, 1, 12, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [7, 1, 7, 7, 20, 20, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 20, 20, 1, 1, 2] 62 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 27]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036162 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(O)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 12, 1, 12, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 3, 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: [23, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 23, 31, 31, 31, 31, 31, 31, 31, 31, 23, 8, 8, 8, 8, 31, 31, 62] 62 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036162 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036162 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036162/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036162/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036162 Building REAL250005036163 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036163' /scratch/stefan/7916117/working/building/REAL250005036163 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036163 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036163/0 /scratch/stefan/7916117/working/building/REAL250005036163 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/749 `/scratch/stefan/7916117/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=NC=CN2N=C1) `REAL250005036163.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036163 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=NC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 64, 88, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 64, 64, 88, 88, 1, 1, 1, 1] 178 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 501 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036163 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=NC=CN2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 22, 8, 1, 1, 1, 1, 1, 1, 1, 88, 178, 178, 178, 178, 178, 178, 178, 178, 87, 22, 22, 8, 8, 178, 178, 178, 178] 178 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036163 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036163 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036163/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036163 Building REAL250005036164 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036164' /scratch/stefan/7916117/working/building/REAL250005036164 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036164 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036164/0 /scratch/stefan/7916117/working/building/REAL250005036164 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/750 `/scratch/stefan/7916117/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC2=NNC=C2C=C1)NCCC1=NC(=O)O[N-]1) `REAL250005036164.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036164 none O=C(CC1=CC2=NNC=C2C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [51, 51, 51, 128, 201, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 201, 201, 201, 51, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 633 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036164 none O=C(CC1=CC2=NNC=C2C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 8, 8, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 74, 86, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 15, 74, 74, 86, 86] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27] set([0, 1, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 522 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036164 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036164 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036164/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036164 Building REAL250005036165 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036165' /scratch/stefan/7916117/working/building/REAL250005036165 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036165 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036165/0 /scratch/stefan/7916117/working/building/REAL250005036165 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/751 `/scratch/stefan/7916117/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC=C1CCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036165.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036165 none CN1C=NC=C1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 162, 157, 60, 60, 60, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 162, 162, 157, 157, 60, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036165 none CN1C=NC=C1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 8, 29, 29, 29, 109, 116, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 6, 6, 8, 8, 29, 110, 110, 116, 116] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036165 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036165 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036165/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036165 Building REAL250005036166 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036166' /scratch/stefan/7916117/working/building/REAL250005036166 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036166 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036166/0 /scratch/stefan/7916117/working/building/REAL250005036166 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/752 `/scratch/stefan/7916117/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC(=O)NC1CC1)NCCC1=NC(=O)O[N-]1) `REAL250005036166.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036166 none O=C(CC(=O)NC1CC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [49, 49, 49, 116, 140, 140, 140, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 116, 116, 140, 201, 201, 201, 201, 201, 49, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 821 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036166 none O=C(CC(=O)NC1CC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [52, 31, 6, 6, 6, 1, 1, 1, 1, 52, 52, 123, 129, 201, 201, 201, 201, 201, 31, 31, 6, 1, 1, 1, 1, 1, 52, 123, 123, 129, 129] 201 rigid atoms, others: [5, 6, 7, 8, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30]) total number of confs: 654 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036166 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036166 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036166/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036166 Building REAL250005036167 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036167' /scratch/stefan/7916117/working/building/REAL250005036167 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036167 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036167/0 /scratch/stefan/7916117/working/building/REAL250005036167 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/753 `/scratch/stefan/7916117/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005036167.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036167 none CC[C@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 162, 162, 162, 162, 162, 58, 162, 58, 58, 19, 9, 1, 1, 1, 1, 1, 1, 1, 162, 162, 173, 201, 201, 201, 201, 162, 162, 162, 162, 58, 19, 19, 9, 9, 162, 162, 162, 162] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 829 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036167 none CC[C@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 58, 72, 162, 162, 162, 162, 162, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 12, 58, 58, 72, 72, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 38, 37, 19, 20, 36, 26, 27, 28, 29, 35] set([0, 32, 34, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 30, 31]) total number of confs: 416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036167 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036167 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036167/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036167 Building REAL250005036168 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036168' /scratch/stefan/7916117/working/building/REAL250005036168 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036168 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036168/0 /scratch/stefan/7916117/working/building/REAL250005036168 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/754 `/scratch/stefan/7916117/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C)CC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036168.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036168 none CC(C)C1(C)CC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 200, 201, 200, 200, 200, 97, 98, 98, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 200, 200, 97, 25, 25, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 629 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036168 none CC(C)C1(C)CC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 1, 5, 1, 1, 1, 1, 1, 8, 8, 8, 41, 66, 200, 200, 200, 200, 200, 6, 6, 6, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 8, 41, 41, 66, 66] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 489 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036168 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036168 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036168/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036168 Building REAL250005036169 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036169' /scratch/stefan/7916117/working/building/REAL250005036169 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036169 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036169/0 /scratch/stefan/7916117/working/building/REAL250005036169 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/755 `/scratch/stefan/7916117/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C12CC(C(F)(F)F)(C1)C2) `REAL250005036169.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036169 none O=C(NCCC1=NC(=O)O[N-]1)C12CC(C(F)(F)F)(C1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 15, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 6, 6, 32, 41, 76, 76, 76, 76, 76, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 32, 32, 41, 41, 1, 1, 1, 1, 1, 1] 76 rigid atoms, others: [1, 11, 12, 13, 14, 18, 19, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 20, 21, 22, 23, 24]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036169 none O=C(NCCC1=NC(=O)O[N-]1)C12CC(C(F)(F)F)(C1)C2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 15, 15, 15, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 39, 17, 7, 1, 1, 1, 1, 1, 1, 1, 39, 76, 76, 76, 76, 76, 76, 76, 76, 39, 17, 17, 7, 7, 76, 76, 76, 76, 76, 76] 76 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036169 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036169 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036169/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036169 Building REAL250005036170 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036170' /scratch/stefan/7916117/working/building/REAL250005036170 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036170 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036170/0 /scratch/stefan/7916117/working/building/REAL250005036170 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/756 `/scratch/stefan/7916117/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(Cl)=N1) `REAL250005036170.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036170 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(Cl)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 16, 8, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [12, 1, 12, 12, 76, 107, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 13, 75, 75, 107, 107, 1] 160 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 524 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036170 none O=C(NCCC1=NC(=O)O[N-]1)C1=CSC(Cl)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 1, 16, 8, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [96, 96, 24, 8, 1, 1, 1, 1, 1, 1, 1, 96, 160, 160, 160, 160, 160, 95, 24, 24, 8, 8, 160] 160 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036170 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036170 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036170/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036170 Building REAL250005036171 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036171' /scratch/stefan/7916117/working/building/REAL250005036171 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036171 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036171/0 /scratch/stefan/7916117/working/building/REAL250005036171 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/757 `/scratch/stefan/7916117/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=COC(CC2CC2)=N1) `REAL250005036171.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036171 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 22, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 7, 23, 23, 1, 5, 16, 16, 22, 22, 1, 7, 7, 23, 23, 23, 23, 23] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 231 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036171 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 21, 7, 1, 1, 1, 1, 1, 1, 1, 66, 80, 80, 80, 80, 156, 201, 201, 80, 66, 21, 21, 7, 7, 80, 156, 156, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 814 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036171 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 23, 34, 34, 98, 122, 201, 201, 201, 201, 201, 23, 23, 23, 5, 1, 1, 1, 1, 23, 34, 98, 98, 122, 122, 23, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 613 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036171 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036171 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036171/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036171 Building REAL250005036172 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036172' /scratch/stefan/7916117/working/building/REAL250005036172 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036172 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036172/0 /scratch/stefan/7916117/working/building/REAL250005036172 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/758 `/scratch/stefan/7916117/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005036172.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036172 none COCCN1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 181, 91, 91, 91, 91, 73, 73, 73, 24, 8, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 181, 181, 91, 91, 73, 24, 24, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036172 none COCCN1C=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [21, 11, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 15, 21, 91, 91, 91, 91, 91, 1, 21, 21, 21, 11, 11, 7, 7, 1, 1, 3, 15, 15, 21, 21] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 19, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 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/7916117/working/building/REAL250005036172 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036172 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036172/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036172 Building REAL250005036173 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036173' /scratch/stefan/7916117/working/building/REAL250005036173 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036173 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036173/0 /scratch/stefan/7916117/working/building/REAL250005036173 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/759 `/scratch/stefan/7916117/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C) `REAL250005036173.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036173 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 173, 173, 173, 98, 99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 175, 175, 175, 173, 98, 24, 24, 8, 8, 173, 173, 173] 175 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 419 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: REAL250005036173 none COC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [10, 1, 1, 1, 1, 1, 11, 11, 11, 51, 68, 173, 173, 173, 173, 173, 1, 1, 1, 10, 10, 10, 1, 11, 51, 51, 68, 68, 2, 2, 2] 175 rigid atoms, others: [1, 2, 3, 4, 5, 16, 17, 18, 22] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 427 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036173 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036173 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036173/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036173 Building REAL250005036174 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036174' /scratch/stefan/7916117/working/building/REAL250005036174 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036174 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036174/0 /scratch/stefan/7916117/working/building/REAL250005036174 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/760 `/scratch/stefan/7916117/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036174.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036174 none CNC(=O)CCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 107, 127, 93, 71, 81, 43, 43, 43, 17, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 107, 107, 92, 92, 91, 91, 81, 81, 43, 17, 17, 8, 8] 127 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 688 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036174 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036174 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036174/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036174 Building REAL250005036175 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036175' /scratch/stefan/7916117/working/building/REAL250005036175 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036175 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036175/0 /scratch/stefan/7916117/working/building/REAL250005036175 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/761 `/scratch/stefan/7916117/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CNC=C(Cl)C1=O) `REAL250005036175.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036175 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNC=C(Cl)C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 16, 1, 11, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 76, 112, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 13, 76, 76, 112, 112, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 608 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036175 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNC=C(Cl)C1=O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 16, 1, 11, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 24, 8, 1, 1, 1, 1, 1, 1, 1, 109, 201, 201, 201, 201, 201, 201, 201, 109, 24, 24, 8, 8, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 463 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036175 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036175 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036175/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036175 Building REAL250005036176 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036176' /scratch/stefan/7916117/working/building/REAL250005036176 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036176 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036176/0 /scratch/stefan/7916117/working/building/REAL250005036176 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/762 `/scratch/stefan/7916117/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=C2CCCCC2=NN1)NCCC1=NC(=O)O[N-]1) `REAL250005036176.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036176 none O=C(CC1=C2CCCCC2=NN1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 120, 201, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 46, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 593 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036176 none O=C(CC1=C2CCCCC2=NN1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 1, 8, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 107, 109, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 107, 107, 109, 109] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 35, 36, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 568 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036176 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036176/1 /scratch/stefan/7916117/working/building/REAL250005036176 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/763 `/scratch/stefan/7916117/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NNC2=C1CCCC2)NCCC1=NC(=O)O[N-]1) `REAL250005036176.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036176 none O=C(CC1=NNC2=C1CCCC2)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 52, 52, 168, 201, 201, 201, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 168, 168, 201, 201, 201, 201, 201, 201, 201, 201, 201, 52, 19, 19, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036176 none O=C(CC1=NNC2=C1CCCC2)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 87, 99, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 87, 87, 99, 99] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 34, 35, 36, 33, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036176 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036176 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036176/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036176/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036176 Building REAL250005036177 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036177' /scratch/stefan/7916117/working/building/REAL250005036177 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036177 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036177/0 /scratch/stefan/7916117/working/building/REAL250005036177 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/764 `/scratch/stefan/7916117/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(O)=C1O) `REAL250005036177.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036177/0/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: REAL250005036177 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(O)=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 12, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 4, 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: [7, 1, 7, 7, 29, 32, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 29, 32, 32, 1, 1, 1, 2, 2] 268 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 27, 28]) total number of confs: 179 number of broken/clashed sets: 105 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036177 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(O)=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 12, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 4, 7, 4, 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: [45, 45, 19, 8, 1, 1, 1, 1, 1, 1, 1, 45, 67, 67, 67, 67, 67, 67, 67, 45, 19, 19, 8, 8, 67, 67, 67, 134, 134] 268 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 466 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036177 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036177 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036177/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036177 Building REAL250005036178 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036178' /scratch/stefan/7916117/working/building/REAL250005036178 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036178 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036178/0 /scratch/stefan/7916117/working/building/REAL250005036178 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/765 `/scratch/stefan/7916117/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CNC(=O)C([N+](=O)[O-])=C1) `REAL250005036178.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036178 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNC(=O)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 11, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 41, 66, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 41, 41, 66, 66, 1, 1, 1] 151 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25]) 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: REAL250005036178 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNC(=O)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 11, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 22, 8, 1, 1, 1, 1, 1, 1, 1, 83, 151, 151, 151, 151, 151, 151, 151, 151, 151, 82, 22, 22, 8, 8, 151, 151, 151] 151 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036178 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036178/1 /scratch/stefan/7916117/working/building/REAL250005036178 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/766 `/scratch/stefan/7916117/working/3D/766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C[N-]C(=O)C([N+](=O)[O-])=C1) `REAL250005036178.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036178 none O=C(NCCC1=NC(=O)O[N-]1)C1=C[N-]C(=O)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 11, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 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, 1, 7, 7, 37, 45, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 37, 37, 45, 45, 1, 1] 96 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 20, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036178 none O=C(NCCC1=NC(=O)O[N-]1)C1=C[N-]C(=O)C([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 11, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 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: [50, 50, 20, 8, 1, 1, 1, 1, 1, 1, 1, 50, 96, 96, 96, 96, 96, 96, 96, 96, 96, 49, 20, 20, 8, 8, 96, 96] 96 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036178 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036178 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036178/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036178/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036178 Building REAL250005036179 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036179' /scratch/stefan/7916117/working/building/REAL250005036179 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036179 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036179/0 /scratch/stefan/7916117/working/building/REAL250005036179 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/767 `/scratch/stefan/7916117/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CNC(=S)N1) `REAL250005036179.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036179 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNC(=S)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'S.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 14, 8, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 3, 4, 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: [12, 1, 12, 12, 54, 77, 131, 131, 131, 131, 131, 1, 1, 1, 1, 1, 1, 12, 54, 54, 77, 77, 1, 1, 1] 131 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036179 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNC(=S)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'S.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 14, 8, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 3, 4, 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: [75, 75, 20, 8, 1, 1, 1, 1, 1, 1, 1, 75, 131, 131, 131, 131, 131, 75, 20, 20, 8, 8, 131, 131, 131] 131 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036179 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036179 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036179/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036179 Building REAL250005036180 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036180' /scratch/stefan/7916117/working/building/REAL250005036180 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036180 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036180/0 /scratch/stefan/7916117/working/building/REAL250005036180 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/768 `/scratch/stefan/7916117/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC2=CC=NC=C21) `REAL250005036180.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036180 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC2=CC=NC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [10, 1, 10, 10, 55, 87, 191, 191, 191, 191, 191, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 55, 55, 87, 87, 1, 1, 1, 1, 1] 191 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 526 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036180 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NC2=CC=NC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [97, 97, 23, 8, 1, 1, 1, 1, 1, 1, 1, 97, 191, 191, 191, 191, 191, 191, 191, 191, 191, 97, 23, 23, 8, 8, 191, 191, 191, 191, 191] 191 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036180 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036180 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036180/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036180 Building REAL250005036181 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036181' /scratch/stefan/7916117/working/building/REAL250005036181 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036181 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036181/0 /scratch/stefan/7916117/working/building/REAL250005036181 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/769 `/scratch/stefan/7916117/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036181.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036181 none CCN1N=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [197, 148, 148, 148, 148, 148, 89, 89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 197, 201, 201, 201, 201, 148, 148, 88, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 704 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: REAL250005036181 none CCN1N=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 42, 56, 148, 148, 148, 148, 148, 6, 6, 6, 6, 6, 1, 1, 10, 42, 42, 56, 56] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 23, 24] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 370 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036181 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036181 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036181/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036181 Building REAL250005036182 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036182' /scratch/stefan/7916117/working/building/REAL250005036182 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036182 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036182/0 /scratch/stefan/7916117/working/building/REAL250005036182 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/770 `/scratch/stefan/7916117/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C([N+](=O)[O-])C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036182.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036182 none CN1N=C([N+](=O)[O-])C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 8, 11, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 161, 161, 161, 161, 161, 87, 87, 87, 23, 8, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 87, 23, 23, 8, 8] 161 rigid atoms, others: [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]) total number of confs: 392 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: REAL250005036182 none CN1N=C([N+](=O)[O-])C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 8, 11, 11, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 13, 73, 98, 161, 161, 161, 161, 161, 2, 2, 2, 1, 13, 73, 73, 98, 98] 161 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 23] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 512 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036182 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036182 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036182/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036182 Building REAL250005036183 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036183' /scratch/stefan/7916117/working/building/REAL250005036183 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036183 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036183/0 /scratch/stefan/7916117/working/building/REAL250005036183 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/771 `/scratch/stefan/7916117/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C=CC=C1F) `REAL250005036183.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036183 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 66, 96, 189, 189, 189, 189, 189, 1, 1, 1, 1, 1, 1, 1, 1, 13, 66, 66, 96, 96, 2, 1, 1, 1] 378 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24]) total number of confs: 552 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: REAL250005036183 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(O)C=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 24, 8, 1, 1, 1, 1, 1, 1, 1, 89, 189, 189, 189, 189, 189, 189, 189, 88, 24, 24, 8, 8, 378, 189, 189, 189] 378 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 794 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036183 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036183/1 /scratch/stefan/7916117/working/building/REAL250005036183 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/772 `/scratch/stefan/7916117/working/3D/772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C([O-])C=CC=C1F) `REAL250005036183.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036183 none O=C(NCCC1=NC(=O)O[N-]1)C1=C([O-])C=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 8, 18, 18, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 1, 1, 1] 29 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005036183 none O=C(NCCC1=NC(=O)O[N-]1)C1=C([O-])C=CC=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 1, 1, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 8, 8, 1, 1, 1, 1, 1, 1, 1, 19, 29, 29, 29, 19, 29, 29, 29, 19, 8, 8, 8, 8, 29, 29, 29] 29 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036183 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036183 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036183/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036183/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036183 Building REAL250005036184 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036184' /scratch/stefan/7916117/working/building/REAL250005036184 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036184 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036184/0 /scratch/stefan/7916117/working/building/REAL250005036184 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/773 `/scratch/stefan/7916117/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036184.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036184 none CC1=CN=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 117, 53, 53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 117, 117, 53, 17, 17, 8, 8, 201] 201 rigid atoms, others: [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]) 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: REAL250005036184 none CC1=CN=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 78, 86, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 6, 6, 17, 78, 78, 86, 86, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 22, 23, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 522 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036184 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036184 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036184/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036184 Building REAL250005036185 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036185' /scratch/stefan/7916117/working/building/REAL250005036185 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036185 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036185/0 /scratch/stefan/7916117/working/building/REAL250005036185 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/774 `/scratch/stefan/7916117/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N(C)C=C1) `REAL250005036185.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036185 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 97, 97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 97, 24, 24, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 459 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: REAL250005036185 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N(C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 11, 11, 11, 53, 81, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 11, 53, 53, 81, 81, 2, 2, 2, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 529 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036185 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036185 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036185/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036185 Building REAL250005036186 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036186' /scratch/stefan/7916117/working/building/REAL250005036186 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036186 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036186/0 /scratch/stefan/7916117/working/building/REAL250005036186 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/775 `/scratch/stefan/7916117/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=N1) `REAL250005036186.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036186 none CCCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 178, 86, 82, 86, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 201, 201, 201, 201, 201, 199, 199, 178, 178, 86, 49, 17, 17, 8, 8, 86, 86, 86] 201 rigid atoms, others: [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, 36, 37, 38]) 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: REAL250005036186 none CCCCN1C=C(C(=O)NCCC2=NC(=O)O[N-]2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 16, 8, 1, 1, 1, 1, 1, 3, 3, 3, 16, 19, 86, 86, 86, 86, 86, 1, 1, 1, 24, 24, 24, 24, 24, 16, 16, 8, 8, 1, 3, 15, 15, 19, 19, 2, 2, 2] 201 rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 20, 30] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036186 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036186 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036186/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036186 Building REAL250005036187 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036187' /scratch/stefan/7916117/working/building/REAL250005036187 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036187 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036187/0 /scratch/stefan/7916117/working/building/REAL250005036187 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/776 `/scratch/stefan/7916117/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C2C=CC=CC2=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036187.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036187 none CN1N=C2C=CC=CC2=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 186, 187, 187, 187, 187, 187, 187, 89, 89, 89, 22, 8, 1, 1, 1, 1, 1, 1, 1, 187, 187, 187, 187, 187, 187, 187, 88, 22, 22, 8, 8] 187 rigid atoms, others: [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]) total number of confs: 425 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: REAL250005036187 none CN1N=C2C=CC=CC2=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 59, 82, 187, 187, 187, 187, 187, 2, 2, 2, 1, 1, 1, 1, 12, 59, 59, 82, 82] 187 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27] set([32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31]) total number of confs: 502 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036187 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036187 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036187/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036187 Building REAL250005036188 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036188' /scratch/stefan/7916117/working/building/REAL250005036188 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036188 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036188/0 /scratch/stefan/7916117/working/building/REAL250005036188 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/777 `/scratch/stefan/7916117/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C1=O) `REAL250005036188.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036188 none CN1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 193, 110, 110, 110, 24, 8, 1, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 193, 193, 193, 193, 193, 110, 24, 24, 8, 8] 193 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 583 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: REAL250005036188 none CN1CCC(C(=O)NCCC2=NC(=O)O[N-]2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 13, 13, 13, 71, 107, 193, 193, 193, 193, 193, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 13, 71, 71, 107, 107] 193 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 21, 22, 23, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 26, 27, 28, 29, 30]) total number of confs: 588 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036188 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036188 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036188/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036188 Building REAL250005036189 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036189' /scratch/stefan/7916117/working/building/REAL250005036189 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036189 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036189/0 /scratch/stefan/7916117/working/building/REAL250005036189 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/778 `/scratch/stefan/7916117/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1) `REAL250005036189.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036189 none COC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 97, 97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 201, 201, 201, 97, 25, 25, 8, 8, 181, 181, 181, 181, 181, 181, 181, 181, 181, 181] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: REAL250005036189 none COC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 5, 5, 5, 29, 53, 181, 181, 181, 181, 181, 1, 1, 1, 1, 1, 10, 10, 10, 5, 29, 29, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 36, 33, 34, 14, 15, 16, 17, 18, 35, 27, 28, 29, 30, 31] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036189 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036189 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036189/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036189 Building REAL250005036190 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036190' /scratch/stefan/7916117/working/building/REAL250005036190 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036190 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036190/0 /scratch/stefan/7916117/working/building/REAL250005036190 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/779 `/scratch/stefan/7916117/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036190.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036190 none CC1(C)CCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 80, 80, 52, 52, 52, 22, 8, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 52, 22, 22, 8, 8] 80 rigid atoms, others: [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]) total number of confs: 301 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: REAL250005036190 none CC1(C)CCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 20, 29, 80, 80, 80, 80, 80, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 20, 20, 29, 29] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 202 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036190 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036190 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036190/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036190 Building REAL250005036191 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036191' /scratch/stefan/7916117/working/building/REAL250005036191 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036191 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036191/0 /scratch/stefan/7916117/working/building/REAL250005036191 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/780 `/scratch/stefan/7916117/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(CC2CC2)=N1) `REAL250005036191.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036191 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [76, 76, 41, 41, 41, 15, 7, 1, 1, 1, 1, 1, 1, 1, 76, 76, 76, 166, 201, 201, 76, 76, 76, 76, 41, 15, 15, 7, 7, 166, 166, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 763 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036191 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 17, 18, 76, 76, 76, 76, 76, 1, 1, 1, 9, 29, 29, 1, 2, 2, 2, 3, 17, 17, 18, 18, 9, 9, 29, 29, 29, 29, 29] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036191 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [29, 29, 29, 29, 59, 59, 59, 133, 133, 201, 201, 201, 201, 201, 29, 5, 1, 1, 1, 1, 29, 29, 29, 29, 59, 133, 133, 133, 133, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 623 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036191 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036191 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036191/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036191 Building REAL250005036192 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036192' /scratch/stefan/7916117/working/building/REAL250005036192 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036192 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036192/0 /scratch/stefan/7916117/working/building/REAL250005036192 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/781 `/scratch/stefan/7916117/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC(CC(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005036192.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036192 none CCOC1CC(CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 183, 183, 183, 135, 43, 43, 43, 17, 8, 1, 1, 1, 1, 1, 1, 1, 183, 201, 201, 201, 201, 201, 183, 183, 183, 183, 135, 135, 43, 17, 17, 8, 8, 183, 183] 201 rigid atoms, others: [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, 36]) total number of confs: 726 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036192 none CCOC1CC(CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 4, 1, 1, 1, 1, 1, 6, 26, 26, 26, 86, 88, 183, 183, 183, 183, 183, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 26, 86, 86, 88, 88, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 18, 35, 24, 25, 26, 27, 36] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036192 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036192 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036192/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036192 Building REAL250005036193 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036193' /scratch/stefan/7916117/working/building/REAL250005036193 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036193 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036193/0 /scratch/stefan/7916117/working/building/REAL250005036193 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/782 `/scratch/stefan/7916117/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C2CC2)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036193.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036193 none CC1=NOC(C2CC2)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [8, 8, 8, 8, 1, 1, 1, 1, 8, 8, 42, 42, 42, 103, 107, 201, 201, 201, 201, 201, 8, 8, 8, 1, 1, 1, 1, 1, 42, 103, 103, 107, 107] 201 rigid atoms, others: [4, 5, 6, 7, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32]) total number of confs: 521 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036193 none CC1=NOC(C2CC2)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 11, 44, 49, 142, 142, 142, 142, 142, 2, 2, 2, 8, 8, 8, 8, 8, 11, 44, 44, 49, 49] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036193 none CC1=NOC(C2CC2)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [142, 142, 142, 142, 142, 142, 201, 201, 53, 53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 201, 201, 201, 201, 201, 53, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 544 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036193 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036193 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036193/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036193 Building REAL250005036194 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036194' /scratch/stefan/7916117/working/building/REAL250005036194 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036194 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036194/0 /scratch/stefan/7916117/working/building/REAL250005036194 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/783 `/scratch/stefan/7916117/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036194.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036194 none CN1C=NC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 163, 60, 60, 60, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 163, 163, 60, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 675 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: REAL250005036194 none CN1C=NC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 29, 101, 103, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 5, 5, 29, 101, 101, 103, 103] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 543 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036194 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036194 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036194/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036194 Building REAL250005036195 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036195' /scratch/stefan/7916117/working/building/REAL250005036195 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036195 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036195/0 /scratch/stefan/7916117/working/building/REAL250005036195 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/784 `/scratch/stefan/7916117/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NNC2=C1CCCCC2) `REAL250005036195.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036195 none O=C(NCCC1=NC(=O)O[N-]1)C1=NNC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 61, 87, 186, 186, 187, 186, 186, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 61, 61, 87, 87, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 187 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 507 number of broken/clashed sets: 187 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036195 none O=C(NCCC1=NC(=O)O[N-]1)C1=NNC2=C1CCCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 21, 8, 1, 1, 1, 1, 1, 1, 1, 97, 186, 186, 187, 187, 187, 187, 187, 187, 187, 96, 22, 21, 8, 8, 186, 187, 187, 187, 187, 187, 187, 187, 187, 187, 187] 187 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 431 number of broken/clashed sets: 187 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036195 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036195/1 /scratch/stefan/7916117/working/building/REAL250005036195 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/785 `/scratch/stefan/7916117/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2CCCCCC2=NN1) `REAL250005036195.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036195 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2CCCCCC2=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 5, 5, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 56, 80, 179, 179, 179, 180, 180, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 56, 56, 81, 81, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 180 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 494 number of broken/clashed sets: 180 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036195 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2CCCCCC2=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 5, 5, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 23, 8, 1, 1, 1, 1, 1, 1, 1, 94, 180, 180, 180, 180, 180, 180, 180, 179, 179, 93, 23, 23, 8, 8, 180, 180, 180, 180, 180, 180, 180, 180, 180, 180, 179] 180 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 409 number of broken/clashed sets: 180 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036195 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036195 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036195/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036195/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036195 Building REAL250005036196 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036196' /scratch/stefan/7916117/working/building/REAL250005036196 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036196 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036196/0 /scratch/stefan/7916117/working/building/REAL250005036196 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/786 `/scratch/stefan/7916117/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005036196.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036196 none COC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 18, 18, 18, 75, 100, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 16, 16, 16, 6, 6, 6, 18, 75, 75, 100, 100, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 35, 36, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL250005036196 none COC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 163, 92, 163, 93, 93, 22, 8, 1, 1, 1, 1, 1, 1, 1, 163, 201, 201, 178, 201, 201, 180, 180, 180, 163, 163, 163, 92, 22, 22, 8, 8, 201, 201, 200, 201, 201] 201 rigid atoms, others: [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, 33, 34, 35, 36]) total number of confs: 822 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036196 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036196 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036196/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036196 Building REAL250005036197 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036197' /scratch/stefan/7916117/working/building/REAL250005036197 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036197 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036197/0 /scratch/stefan/7916117/working/building/REAL250005036197 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/787 `/scratch/stefan/7916117/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(O)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036197.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036197 none N#CC1=CC(O)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 171, 171, 171, 171, 73, 73, 73, 20, 8, 1, 1, 1, 1, 1, 1, 1, 171, 171, 342, 171, 73, 20, 20, 8, 8, 171] 342 rigid atoms, others: [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]) 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: REAL250005036197 none N#CC1=CC(O)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 342 conformations in input total number of sets (complete confs): 342 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 41, 66, 171, 171, 171, 171, 171, 1, 1, 2, 1, 7, 41, 41, 66, 66, 1] 342 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 22, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, 24, 25, 26, 27]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036197 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036197/1 /scratch/stefan/7916117/working/building/REAL250005036197 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/788 `/scratch/stefan/7916117/working/3D/788' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC([O-])=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036197.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036197 none N#CC1=CC([O-])=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 85, 85, 85, 46, 46, 46, 20, 8, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 45, 20, 20, 8, 8, 85] 85 rigid atoms, others: [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]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036197 none N#CC1=CC([O-])=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 27, 35, 85, 85, 85, 85, 85, 1, 1, 1, 7, 27, 27, 35, 35, 1] 85 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036197 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036197 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036197/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036197/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036197 Building REAL250005036198 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036198' /scratch/stefan/7916117/working/building/REAL250005036198 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036198 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036198/0 /scratch/stefan/7916117/working/building/REAL250005036198 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/789 `/scratch/stefan/7916117/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCC2=NC(=O)O[N-]2)CNC(=O)C1) `REAL250005036198.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036198 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 6, 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, 95, 95, 95, 22, 8, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 172, 172, 172, 172, 95, 23, 23, 8, 8, 172, 172, 172, 172, 172] 172 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 529 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: REAL250005036198 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 7, 7, 7, 43, 71, 172, 172, 172, 172, 172, 1, 1, 1, 1, 1, 2, 2, 2, 7, 43, 43, 71, 71, 1, 1, 1, 1, 1] 172 rigid atoms, others: [0, 1, 2, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 463 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036198 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036198 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036198/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036198 Building REAL250005036199 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036199' /scratch/stefan/7916117/working/building/REAL250005036199 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036199 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036199/0 /scratch/stefan/7916117/working/building/REAL250005036199 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/790 `/scratch/stefan/7916117/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036199.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036199 none COCC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 128, 128, 128, 128, 128, 105, 58, 58, 58, 17, 8, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 128, 128, 128, 105, 105, 58, 17, 17, 8, 8, 128] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 929 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036199 none COCC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 31, 34, 128, 128, 128, 128, 128, 1, 21, 21, 21, 7, 7, 1, 1, 1, 2, 2, 9, 31, 31, 34, 34, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 36, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036199 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036199 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036199/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036199 Building REAL250005036200 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036200' /scratch/stefan/7916117/working/building/REAL250005036200 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036200 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036200/0 /scratch/stefan/7916117/working/building/REAL250005036200 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/791 `/scratch/stefan/7916117/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005036200.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036200 none C=CCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 3, 10, 10, 10, 45, 49, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 15, 15, 15, 6, 6, 3, 10, 45, 45, 49, 49, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 3, 36, 35, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 377 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036200 none C=CCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 180, 139, 53, 53, 53, 17, 7, 1, 1, 1, 1, 1, 1, 1, 139, 160, 160, 139, 160, 160, 181, 181, 181, 180, 180, 139, 53, 17, 17, 7, 7, 160, 160, 139, 160, 160] 201 rigid atoms, others: [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, 33, 34, 35, 36]) total number of confs: 879 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036200 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036200 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036200/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036200 Building REAL250005036201 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036201' /scratch/stefan/7916117/working/building/REAL250005036201 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036201 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036201/0 /scratch/stefan/7916117/working/building/REAL250005036201 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/792 `/scratch/stefan/7916117/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC=C1CCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036201.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036201 none CN1N=CC=C1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 145, 145, 60, 60, 60, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 145, 145, 145, 145, 60, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 665 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036201 none CN1N=CC=C1CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 32, 32, 109, 118, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 6, 6, 6, 6, 32, 110, 110, 118, 118] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 580 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036201 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036201 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036201/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036201 Building REAL250005036202 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036202' /scratch/stefan/7916117/working/building/REAL250005036202 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036202 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036202/0 /scratch/stefan/7916117/working/building/REAL250005036202 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/793 `/scratch/stefan/7916117/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](OCC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036202.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036202 none C[C@H](OCC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 37, 89, 89, 109, 157, 201, 201, 167, 201, 201, 37, 37, 8, 8, 1, 1, 1, 1, 1, 1, 1, 89, 89, 87, 157, 157, 201, 201, 201, 201, 201, 37, 8, 8, 8, 8] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 890 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036202 none C[C@H](OCC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [34, 12, 34, 3, 1, 1, 1, 1, 1, 1, 1, 34, 63, 63, 63, 108, 108, 201, 201, 201, 201, 201, 34, 34, 34, 3, 3, 1, 1, 1, 1, 1, 63, 108, 108, 108, 108] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36]) total number of confs: 613 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036202 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036202 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036202/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036202 Building REAL250005036203 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036203' /scratch/stefan/7916117/working/building/REAL250005036203 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036203 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036203/0 /scratch/stefan/7916117/working/building/REAL250005036203 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/794 `/scratch/stefan/7916117/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NC(C2CC2)=C1) `REAL250005036203.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036203 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 27, 31, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 1, 10, 10, 1, 5, 27, 27, 31, 31, 1, 1, 10, 10, 10, 10, 10, 1] 201 rigid atoms, others: [1, 33, 11, 12, 13, 14, 15, 16, 17, 20, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 257 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036203 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 17, 8, 1, 1, 1, 1, 1, 1, 1, 56, 127, 127, 127, 127, 127, 127, 201, 201, 127, 56, 17, 17, 8, 8, 127, 127, 201, 201, 201, 201, 201, 127] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 551 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036203 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NC(C2CC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 10, 28, 28, 95, 97, 201, 201, 201, 201, 201, 10, 9, 10, 10, 10, 1, 1, 1, 1, 10, 28, 95, 95, 97, 97, 9, 10, 1, 1, 1, 1, 1, 10] 201 rigid atoms, others: [32, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 33]) total number of confs: 516 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036203 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036203 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036203/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036203 Building REAL250005036204 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036204' /scratch/stefan/7916117/working/building/REAL250005036204 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036204 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036204/0 /scratch/stefan/7916117/working/building/REAL250005036204 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/795 `/scratch/stefan/7916117/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=N1) `REAL250005036204.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036204 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 48, 48, 48, 20, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 48, 20, 20, 8, 8, 131] 131 rigid atoms, others: [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]) 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: REAL250005036204 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC(Cl)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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, 5, 5, 5, 30, 53, 131, 131, 131, 131, 131, 1, 1, 1, 1, 2, 2, 2, 1, 5, 30, 30, 53, 53, 1] 131 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 22, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036204 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036204 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036204/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036204 Building REAL250005036205 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036205' /scratch/stefan/7916117/working/building/REAL250005036205 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036205 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036205/0 /scratch/stefan/7916117/working/building/REAL250005036205 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/796 `/scratch/stefan/7916117/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1CC1) `REAL250005036205.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036205 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 41, 53, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 1, 7, 7, 9, 41, 41, 53, 53, 1, 1, 7, 7, 7, 7, 7] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036205 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 21, 8, 1, 1, 1, 1, 1, 1, 1, 68, 155, 155, 155, 155, 155, 201, 201, 68, 21, 21, 8, 8, 155, 155, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036205 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 8, 39, 39, 109, 117, 201, 201, 201, 201, 201, 7, 7, 7, 7, 1, 1, 1, 1, 39, 109, 109, 117, 117, 7, 7, 1, 1, 1, 1, 1] 201 rigid atoms, others: [15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 577 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036205 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036205 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036205/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036205 Building REAL250005036206 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036206' /scratch/stefan/7916117/working/building/REAL250005036206 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036206 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036206/0 /scratch/stefan/7916117/working/building/REAL250005036206 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/797 `/scratch/stefan/7916117/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(OC)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005036206.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036206 none COC(OC)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [199, 167, 78, 167, 199, 79, 79, 79, 61, 61, 61, 18, 8, 1, 1, 1, 1, 1, 1, 1, 78, 199, 199, 199, 167, 199, 199, 199, 79, 79, 60, 19, 18, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 732 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036206 none COC(OC)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [35, 11, 1, 11, 38, 1, 1, 1, 1, 1, 4, 4, 4, 14, 21, 78, 78, 78, 79, 79, 1, 35, 35, 35, 11, 38, 38, 38, 1, 1, 4, 14, 14, 21, 21] 201 rigid atoms, others: [2, 5, 6, 7, 8, 9, 20, 28, 29] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 273 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036206 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036206 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036206/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036206 Building REAL250005036207 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036207' /scratch/stefan/7916117/working/building/REAL250005036207 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036207 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036207/0 /scratch/stefan/7916117/working/building/REAL250005036207 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/798 `/scratch/stefan/7916117/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1C=CCCC1)NCCC1=NC(=O)O[N-]1) `REAL250005036207.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036207 none O=C(CC1C=CCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [63, 63, 63, 183, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 183, 183, 201, 201, 201, 201, 201, 201, 201, 201, 201, 63, 19, 19, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036207 none O=C(CC1C=CCCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 7, 1, 1, 1, 1, 1, 1, 1, 27, 27, 93, 97, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 93, 93, 97, 97] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 521 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036207 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036207 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036207/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036207 Building REAL250005036208 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036208' /scratch/stefan/7916117/working/building/REAL250005036208 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036208 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036208/0 /scratch/stefan/7916117/working/building/REAL250005036208 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/799 `/scratch/stefan/7916117/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=C(F)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036208.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036208 none N#CC1=C(F)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 164, 164, 164, 164, 93, 93, 93, 23, 8, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 93, 23, 23, 8, 8] 164 rigid atoms, others: [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]) total number of confs: 392 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036208 none N#CC1=C(F)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 55, 88, 164, 164, 164, 164, 164, 1, 1, 1, 9, 55, 55, 88, 88] 164 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036208 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036208 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036208/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036208 Building REAL250005036209 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036209' /scratch/stefan/7916117/working/building/REAL250005036209 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036209 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036209/0 /scratch/stefan/7916117/working/building/REAL250005036209 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/800 `/scratch/stefan/7916117/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036209.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036209 none CC1CCCC1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 195, 60, 60, 60, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 60, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 775 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036209 none CC1CCCC1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 5, 26, 26, 26, 88, 95, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 88, 88, 95, 95] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31]) total number of confs: 514 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036209 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036209 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036209/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036209 Building REAL250005036210 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036210' /scratch/stefan/7916117/working/building/REAL250005036210 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036210 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036210/0 /scratch/stefan/7916117/working/building/REAL250005036210 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/801 `/scratch/stefan/7916117/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036210.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036210 none CN1C(=O)CCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 168, 168, 103, 103, 103, 24, 8, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 168, 168, 168, 168, 103, 25, 25, 8, 8] 168 rigid atoms, others: [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]) total number of confs: 531 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: REAL250005036210 none CN1C(=O)CCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 55, 77, 168, 168, 168, 168, 168, 1, 1, 1, 1, 1, 1, 1, 1, 11, 55, 55, 77, 77] 168 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30]) total number of confs: 456 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036210 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036210 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036210/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036210 Building REAL250005036211 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036211' /scratch/stefan/7916117/working/building/REAL250005036211 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036211 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036211/0 /scratch/stefan/7916117/working/building/REAL250005036211 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/802 `/scratch/stefan/7916117/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(F)C=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036211.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036211 none COC1=CC=C(F)C=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 196, 196, 196, 196, 196, 196, 126, 39, 39, 39, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 196, 195, 196, 126, 126, 39, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036211 none COC1=CC=C(F)C=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 29, 103, 103, 196, 196, 196, 196, 196, 4, 4, 4, 1, 1, 1, 5, 5, 29, 103, 103, 103, 103] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26] set([0, 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: 548 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036211 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036211 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036211/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036211 Building REAL250005036212 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036212' /scratch/stefan/7916117/working/building/REAL250005036212 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036212 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036212/0 /scratch/stefan/7916117/working/building/REAL250005036212 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/803 `/scratch/stefan/7916117/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(F)=C1F) `REAL250005036212.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036212 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 15, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [12, 1, 12, 12, 68, 99, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 68, 68, 99, 99, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 576 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036212 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(F)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 15, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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, 22, 8, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 201, 201, 201, 86, 23, 23, 8, 8, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036212 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036212 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036212/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036212 Building REAL250005036213 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036213' /scratch/stefan/7916117/working/building/REAL250005036213 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036213 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036213/0 /scratch/stefan/7916117/working/building/REAL250005036213 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/804 `/scratch/stefan/7916117/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1) `REAL250005036213.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036213 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 22, 22, 22, 80, 94, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 22, 80, 80, 94, 94, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 535 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036213 none CC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', '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'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 67, 67, 67, 20, 8, 1, 1, 1, 1, 1, 1, 1, 169, 201, 201, 171, 201, 201, 169, 169, 169, 169, 67, 20, 20, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 836 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036213 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036213 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036213/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036213 Building REAL250005036214 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036214' /scratch/stefan/7916117/working/building/REAL250005036214 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036214 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036214/0 /scratch/stefan/7916117/working/building/REAL250005036214 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/805 `/scratch/stefan/7916117/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036214.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036214 none CS(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 157, 201, 157, 63, 157, 157, 62, 62, 62, 19, 8, 1, 1, 1, 1, 1, 1, 1, 157, 201, 201, 201, 62, 157, 157, 62, 19, 19, 8, 8, 157] 201 rigid atoms, others: [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]) total number of confs: 699 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036214 none CS(=O)C1=CC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 36, 157, 157, 157, 157, 157, 1, 10, 10, 10, 1, 1, 1, 5, 29, 29, 36, 36, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 19, 23, 24, 25, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036214 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036214 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036214/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036214 Building REAL250005036215 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036215' /scratch/stefan/7916117/working/building/REAL250005036215 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036215 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036215/0 /scratch/stefan/7916117/working/building/REAL250005036215 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/806 `/scratch/stefan/7916117/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(=O)CC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036215.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036215 none CC(NC(=O)CC(C)(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 48, 140, 158, 158, 158, 201, 201, 201, 201, 48, 48, 8, 8, 1, 1, 1, 1, 1, 1, 1, 140, 140, 135, 140, 158, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 47, 8, 8, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 830 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036215 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036215 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036215/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036215 Building REAL250005036216 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036216' /scratch/stefan/7916117/working/building/REAL250005036216 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036216 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036216/0 /scratch/stefan/7916117/working/building/REAL250005036216 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/807 `/scratch/stefan/7916117/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005036216.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036216 none CCOC1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 185, 170, 170, 170, 170, 99, 99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 170, 170, 201, 201, 201, 201, 201, 170, 98, 24, 24, 8, 8, 170] 201 rigid atoms, others: [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]) total number of confs: 536 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036216 none CCOC1=CN=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 42, 60, 169, 169, 169, 169, 169, 1, 1, 19, 19, 19, 19, 19, 1, 9, 42, 42, 60, 61, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 18, 19, 25, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036216 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036216 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036216/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036216 Building REAL250005036217 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036217' /scratch/stefan/7916117/working/building/REAL250005036217 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036217 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036217/0 /scratch/stefan/7916117/working/building/REAL250005036217 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/808 `/scratch/stefan/7916117/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL250005036217.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036217 none N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 125, 46, 46, 46, 18, 8, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 46, 18, 18, 8, 8, 125] 125 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036217 none N#CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 63, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 7, 37, 37, 63, 63, 1] 125 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036217 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036217 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036217/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036217 Building REAL250005036218 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036218' /scratch/stefan/7916117/working/building/REAL250005036218 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036218 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036218/0 /scratch/stefan/7916117/working/building/REAL250005036218 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/809 `/scratch/stefan/7916117/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)OC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036218.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036218 none CC(=O)OC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 182, 63, 182, 182, 63, 63, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 182, 182, 182, 182, 182, 182, 63, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036218 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036218 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036218/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036218 Building REAL250005036219 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036219' /scratch/stefan/7916117/working/building/REAL250005036219 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036219 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036219/0 /scratch/stefan/7916117/working/building/REAL250005036219 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/810 `/scratch/stefan/7916117/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21) `REAL250005036219.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036219 none CN1CCC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 49, 49, 50, 23, 8, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 49, 23, 23, 8, 8, 107, 107] 107 rigid atoms, others: [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]) 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: REAL250005036219 none CN1CCC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 55, 107, 107, 107, 107, 107, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 7, 33, 33, 55, 55, 1, 1] 107 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 34, 18, 19, 20, 24, 25, 26, 27, 28, 35] set([32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 29, 30, 31]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036219 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036219 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036219/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036219 Building REAL250005036220 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036220' /scratch/stefan/7916117/working/building/REAL250005036220 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036220 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036220/0 /scratch/stefan/7916117/working/building/REAL250005036220 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/811 `/scratch/stefan/7916117/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CN(C)C1=O) `REAL250005036220.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036220 none CCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 109, 109, 109, 51, 51, 51, 19, 8, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 201, 201, 201, 201, 201, 109, 51, 19, 19, 8, 8, 109, 109, 109, 109] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 822 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036220 none CCC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 5, 5, 5, 28, 38, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 5, 28, 28, 38, 38, 1, 2, 2, 2] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036220 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036220 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036220/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036220 Building REAL250005036221 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036221' /scratch/stefan/7916117/working/building/REAL250005036221 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036221 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036221/0 /scratch/stefan/7916117/working/building/REAL250005036221 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/812 `/scratch/stefan/7916117/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC1(Cl)Cl)NCCC1=NC(=O)O[N-]1) `REAL250005036221.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036221 none O=C(CC1CC1(Cl)Cl)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'Cl', 'Cl', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 16, 16, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [59, 59, 59, 185, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 185, 185, 201, 201, 201, 59, 19, 19, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 774 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036221 none O=C(CC1CC1(Cl)Cl)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'Cl', 'Cl', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 16, 16, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [37, 5, 1, 1, 1, 1, 1, 1, 37, 37, 117, 119, 201, 201, 201, 200, 201, 5, 5, 1, 1, 1, 37, 117, 117, 119, 119] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 19, 20, 21] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036221 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036221 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036221/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036221 Building REAL250005036222 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036222' /scratch/stefan/7916117/working/building/REAL250005036222 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036222 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036222/0 /scratch/stefan/7916117/working/building/REAL250005036222 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/813 `/scratch/stefan/7916117/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036222.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036222 none CC1=CC(C)=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 165, 165, 91, 91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 165, 165, 91, 24, 24, 8, 8, 165] 165 rigid atoms, others: [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]) total number of confs: 402 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036222 none CC1=CC(C)=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 52, 77, 165, 165, 165, 165, 165, 1, 2, 2, 2, 1, 2, 2, 2, 12, 52, 52, 77, 77, 1] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 22, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 472 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036222 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036222 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036222/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036222 Building REAL250005036223 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036223' /scratch/stefan/7916117/working/building/REAL250005036223 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036223 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036223/0 /scratch/stefan/7916117/working/building/REAL250005036223 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/814 `/scratch/stefan/7916117/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=N1)CCCC2) `REAL250005036223.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036223 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=N1)CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 54, 76, 140, 140, 140, 141, 141, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 53, 53, 76, 76, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 141 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 413 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036223 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(C=N1)CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [69, 69, 20, 8, 1, 1, 1, 1, 1, 1, 1, 69, 141, 141, 141, 140, 140, 141, 141, 141, 141, 68, 20, 20, 8, 8, 141, 140, 141, 141, 141, 141, 141, 141, 141, 141] 141 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036223 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036223 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036223/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036223 Building REAL250005036224 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036224' /scratch/stefan/7916117/working/building/REAL250005036224 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036224 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036224/0 /scratch/stefan/7916117/working/building/REAL250005036224 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/815 `/scratch/stefan/7916117/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SCCO1) `REAL250005036224.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036224 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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, 80, 80, 80, 24, 8, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 112, 112, 80, 25, 25, 8, 8, 112, 112, 112, 112] 112 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036224 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 36, 53, 112, 112, 112, 112, 112, 1, 1, 1, 1, 2, 2, 2, 7, 36, 36, 53, 53, 1, 1, 1, 1] 112 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 26, 27, 28, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036224 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036224 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036224/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036224 Building REAL250005036225 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036225' /scratch/stefan/7916117/working/building/REAL250005036225 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036225 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036225/0 /scratch/stefan/7916117/working/building/REAL250005036225 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/816 `/scratch/stefan/7916117/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C(O)C=C1) `REAL250005036225.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036225 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C(O)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [36, 7, 36, 36, 102, 113, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 1, 36, 102, 102, 113, 113, 1, 1, 2, 1, 1] 402 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 25, 26, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24, 27]) total number of confs: 592 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036225 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C(O)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 19, 8, 1, 1, 1, 1, 1, 1, 1, 75, 143, 143, 201, 201, 201, 201, 201, 201, 74, 19, 19, 8, 8, 201, 201, 402, 201, 201] 402 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 952 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036225 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036225/1 /scratch/stefan/7916117/working/building/REAL250005036225 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/817 `/scratch/stefan/7916117/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C([O-])C=C1) `REAL250005036225.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036225 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C([O-])C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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: [30, 7, 30, 30, 103, 124, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 1, 30, 103, 103, 124, 124, 1, 1, 1, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 22, 23, 24]) 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: REAL250005036225 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=C([O-])C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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: [75, 75, 24, 8, 1, 1, 1, 1, 1, 1, 1, 75, 148, 148, 201, 201, 201, 201, 201, 201, 75, 24, 24, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 562 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036225 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036225 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036225/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036225/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036225 Building REAL250005036226 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036226' /scratch/stefan/7916117/working/building/REAL250005036226 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036226 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036226/0 /scratch/stefan/7916117/working/building/REAL250005036226 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/818 `/scratch/stefan/7916117/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2CC2)=NO1) `REAL250005036226.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036226 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 29, 34, 88, 88, 88, 89, 89, 1, 1, 1, 1, 13, 13, 1, 1, 6, 28, 28, 34, 34, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 11, 12, 13, 14, 17, 18, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036226 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 20, 8, 1, 1, 1, 1, 1, 1, 1, 60, 89, 89, 89, 201, 201, 88, 88, 59, 20, 20, 8, 8, 89, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036226 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(C2CC2)=NO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 5, 5, 8, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 13, 42, 42, 117, 127, 201, 201, 201, 201, 201, 13, 13, 1, 1, 1, 1, 13, 13, 42, 117, 117, 127, 127, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [13, 14, 15, 16, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 604 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036226 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036226 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036226/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036226 Building REAL250005036227 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036227' /scratch/stefan/7916117/working/building/REAL250005036227 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036227 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036227/0 /scratch/stefan/7916117/working/building/REAL250005036227 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/819 `/scratch/stefan/7916117/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C#N)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036227.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036227 none CC1=C(C#N)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 184, 186, 186, 186, 186, 186, 93, 93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 186, 93, 24, 25, 8, 8] 186 rigid atoms, others: [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]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036227 none CC1=C(C#N)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.1', 'N.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 1, 1, 1, 10, 10, 10, 53, 85, 186, 186, 186, 186, 186, 2, 2, 2, 1, 1, 1, 10, 53, 53, 85, 85] 186 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 522 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036227 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036227 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036227/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036227 Building REAL250005036228 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036228' /scratch/stefan/7916117/working/building/REAL250005036228 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036228 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036228/0 /scratch/stefan/7916117/working/building/REAL250005036228 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/820 `/scratch/stefan/7916117/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C#N) `REAL250005036228.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036228 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 55, 55, 55, 20, 8, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 137, 137, 137, 137, 54, 20, 20, 8, 8, 137] 137 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036228 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 7, 7, 7, 41, 63, 137, 137, 137, 137, 137, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 41, 41, 63, 63, 1] 137 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 23, 24, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036228 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036228 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036228/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036228 Building REAL250005036229 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036229' /scratch/stefan/7916117/working/building/REAL250005036229 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036229 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036229/0 /scratch/stefan/7916117/working/building/REAL250005036229 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/821 `/scratch/stefan/7916117/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005036229.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036229 none CCOCC1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 199, 188, 139, 53, 53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 139, 139, 201, 201, 201, 201, 201, 188, 188, 53, 17, 17, 8, 8, 139, 139, 139, 139] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL250005036229 none CCOCC1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [21, 17, 8, 1, 1, 1, 7, 7, 7, 33, 38, 139, 139, 139, 139, 139, 1, 1, 21, 21, 21, 21, 21, 8, 8, 7, 33, 33, 38, 38, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 16, 17, 30, 31] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036229 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036229 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036229/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036229 Building REAL250005036230 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036230' /scratch/stefan/7916117/working/building/REAL250005036230 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036230 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036230/0 /scratch/stefan/7916117/working/building/REAL250005036230 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/822 `/scratch/stefan/7916117/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CN=C21) `REAL250005036230.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036230 none CN1N=NC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 117, 117, 117, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 117, 24, 24, 8, 8, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL250005036230 none CN1N=NC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CN=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 76, 113, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 12, 76, 76, 113, 113, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036230 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036230 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036230/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036230 Building REAL250005036231 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036231' /scratch/stefan/7916117/working/building/REAL250005036231 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036231 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036231/0 /scratch/stefan/7916117/working/building/REAL250005036231 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/823 `/scratch/stefan/7916117/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C)C(C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005036231.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036231 none CC1CC(C)C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 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, 76, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 76, 24, 24, 8, 8] 90 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036231 none CC1CC(C)C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 22, 38, 90, 90, 90, 90, 90, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 4, 22, 22, 38, 38] 90 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 21, 22, 23, 24, 28] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 25, 26, 27, 29, 30, 31]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036231 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036231 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036231/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036231 Building REAL250005036232 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036232' /scratch/stefan/7916117/working/building/REAL250005036232 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036232 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036232/0 /scratch/stefan/7916117/working/building/REAL250005036232 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/824 `/scratch/stefan/7916117/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1=CSC=C1)NCCC1=NC(=O)O[N-]1) `REAL250005036232.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036232 none O=C(COC1=CSC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 14, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [35, 35, 35, 83, 133, 201, 201, 201, 201, 13, 7, 1, 1, 1, 1, 1, 1, 1, 83, 83, 201, 201, 201, 35, 13, 13, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 552 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036232 none O=C(COC1=CSC=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 14, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [70, 18, 6, 1, 1, 1, 1, 1, 1, 70, 70, 137, 137, 201, 201, 201, 201, 201, 18, 18, 1, 1, 1, 70, 137, 137, 137, 137] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 20, 21, 22] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27]) total number of confs: 662 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036232 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036232 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036232/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036232 Building REAL250005036233 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036233' /scratch/stefan/7916117/working/building/REAL250005036233 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036233 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036233/0 /scratch/stefan/7916117/working/building/REAL250005036233 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/825 `/scratch/stefan/7916117/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036233.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036233 none CCC1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 167, 167, 167, 167, 167, 91, 91, 92, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 91, 24, 24, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 747 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036233 none CCC1CCCCC1C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 38, 58, 167, 167, 167, 167, 167, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 38, 38, 58, 58] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036233 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036233 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036233/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036233 Building REAL250005036234 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036234' /scratch/stefan/7916117/working/building/REAL250005036234 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036234 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036234/0 /scratch/stefan/7916117/working/building/REAL250005036234 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/826 `/scratch/stefan/7916117/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC1C1=CC=CC(F)=C1) `REAL250005036234.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036234 none O=C(NCCC1=NC(=O)O[N-]1)C1CC1C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 41, 146, 146, 146, 146, 146, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 31, 31, 41, 41, 1, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [1, 11, 12, 13, 14, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 302 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: REAL250005036234 none O=C(NCCC1=NC(=O)O[N-]1)C1CC1C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 8, 1, 1, 1, 1, 1, 1, 1, 71, 146, 146, 146, 201, 201, 201, 201, 201, 201, 71, 21, 21, 8, 8, 146, 146, 146, 146, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 577 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: REAL250005036234 none O=C(NCCC1=NC(=O)O[N-]1)C1CC1C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 18, 18, 73, 86, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 18, 73, 73, 86, 86, 5, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 506 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036234 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036234 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036234/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036234 Building REAL250005036235 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036235' /scratch/stefan/7916117/working/building/REAL250005036235 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036235 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036235/0 /scratch/stefan/7916117/working/building/REAL250005036235 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/827 `/scratch/stefan/7916117/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CON=C1C1CC1) `REAL250005036235.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036235 none O=C(NCCC1=NC(=O)O[N-]1)C1=CON=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 41, 47, 152, 152, 152, 152, 152, 1, 1, 1, 1, 1, 1, 8, 8, 9, 41, 41, 47, 47, 1, 8, 8, 8, 8, 8] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 322 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036235 none O=C(NCCC1=NC(=O)O[N-]1)C1=CON=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 19, 8, 1, 1, 1, 1, 1, 1, 1, 58, 152, 152, 152, 152, 152, 201, 201, 58, 19, 19, 8, 8, 152, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 522 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036235 none O=C(NCCC1=NC(=O)O[N-]1)C1=CON=C1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 8, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 8, 33, 33, 104, 107, 201, 201, 201, 201, 201, 8, 7, 8, 8, 1, 1, 1, 1, 33, 104, 104, 107, 107, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [15, 16, 17, 18, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24]) total number of confs: 526 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036235 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036235 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036235/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036235 Building REAL250005036236 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036236' /scratch/stefan/7916117/working/building/REAL250005036236 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036236 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036236/0 /scratch/stefan/7916117/working/building/REAL250005036236 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/828 `/scratch/stefan/7916117/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC1=NC(C)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005036236.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036236 none CNC1=NC(C)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 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, 56, 56, 56, 56, 56, 56, 40, 40, 40, 20, 8, 1, 1, 1, 1, 1, 1, 1, 56, 89, 89, 89, 89, 56, 56, 56, 56, 39, 21, 21, 8, 8] 89 rigid atoms, others: [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]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036236 none CNC1=NC(C)=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 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: [4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 8, 28, 30, 56, 56, 56, 56, 56, 1, 4, 4, 4, 4, 2, 2, 2, 1, 9, 28, 28, 30, 30] 89 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 19, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036236 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036236 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036236/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036236 Building REAL250005036237 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036237' /scratch/stefan/7916117/working/building/REAL250005036237 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036237 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036237/0 /scratch/stefan/7916117/working/building/REAL250005036237 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/829 `/scratch/stefan/7916117/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(CC)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036237.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036237 none CCCC(C)(CC)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 183, 134, 61, 134, 134, 152, 61, 61, 19, 8, 1, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 193, 193, 134, 134, 134, 165, 165, 165, 165, 165, 61, 19, 19, 8, 8] 201 rigid atoms, others: [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, 36, 37]) total number of confs: 1210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036237 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036237 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036237/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036237 Building REAL250005036238 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036238' /scratch/stefan/7916117/working/building/REAL250005036238 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036238 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036238/0 /scratch/stefan/7916117/working/building/REAL250005036238 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/830 `/scratch/stefan/7916117/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=COC(C(=O)NCCC2=NC(=O)O[N-]2)=CC1=O) `REAL250005036238.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036238 none COC1=COC(C(=O)NCCC2=NC(=O)O[N-]2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 170, 170, 170, 139, 84, 84, 84, 24, 8, 1, 1, 1, 1, 1, 1, 1, 170, 170, 170, 201, 201, 201, 170, 84, 24, 24, 8, 8, 170] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 466 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036238 none COC1=COC(C(=O)NCCC2=NC(=O)O[N-]2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 58, 74, 170, 170, 170, 170, 170, 1, 1, 1, 4, 4, 4, 1, 9, 57, 57, 74, 74, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 19, 23, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 24, 25, 26, 27, 28]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036238 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036238 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036238/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036238 Building REAL250005036239 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036239' /scratch/stefan/7916117/working/building/REAL250005036239 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036239 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036239/0 /scratch/stefan/7916117/working/building/REAL250005036239 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/831 `/scratch/stefan/7916117/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=NC=C2N=C1) `REAL250005036239.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036239 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=NC=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 31, 55, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 31, 31, 55, 55, 1, 1, 1, 1, 1] 105 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) 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: REAL250005036239 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=NC=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 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: [55, 55, 21, 8, 1, 1, 1, 1, 1, 1, 1, 55, 105, 105, 105, 105, 105, 105, 105, 105, 105, 54, 21, 21, 8, 8, 105, 105, 105, 105, 105] 105 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036239 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036239 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036239/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036239 Building REAL250005036240 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036240' /scratch/stefan/7916117/working/building/REAL250005036240 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036240 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036240/0 /scratch/stefan/7916117/working/building/REAL250005036240 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/832 `/scratch/stefan/7916117/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC2=C1) `REAL250005036240.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036240 none CC1=CN2C=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 131, 64, 65, 65, 21, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 131, 64, 21, 21, 8, 8, 131, 131, 131] 131 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036240 none CC1=CN2C=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 46, 69, 131, 131, 131, 131, 131, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 46, 46, 69, 69, 1, 1, 1] 131 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 17, 18, 19, 20, 24, 25, 33, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036240 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036240 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036240/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036240 Building REAL250005036241 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036241' /scratch/stefan/7916117/working/building/REAL250005036241 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036241 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036241/0 /scratch/stefan/7916117/working/building/REAL250005036241 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/833 `/scratch/stefan/7916117/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=N1) `REAL250005036241.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036241 none CCCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 23, 9, 1, 9, 32, 32, 32, 88, 88, 168, 168, 168, 168, 168, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 23, 23, 9, 32, 88, 88, 88, 88, 1, 1, 1, 1] 201 rigid atoms, others: [19, 34, 3, 36, 37, 15, 16, 17, 18, 35, 20] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 539 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036241 none CCCC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 176, 121, 44, 44, 44, 8, 8, 1, 1, 1, 1, 1, 1, 1, 122, 168, 168, 168, 168, 168, 181, 181, 181, 181, 181, 176, 176, 122, 43, 8, 8, 8, 8, 168, 168, 168, 168] 201 rigid atoms, others: [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, 33, 34, 35, 36, 37]) total number of confs: 837 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036241 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036241 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036241/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036241 Building REAL250005036242 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036242' /scratch/stefan/7916117/working/building/REAL250005036242 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036242 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036242/0 /scratch/stefan/7916117/working/building/REAL250005036242 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/834 `/scratch/stefan/7916117/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=N1) `REAL250005036242.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036242 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [13, 1, 13, 13, 53, 63, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 1, 13, 53, 53, 63, 63, 1, 1, 1] 112 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036242 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(F)C=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 22, 8, 1, 1, 1, 1, 1, 1, 1, 75, 112, 112, 112, 112, 112, 112, 75, 22, 22, 8, 8, 112, 112, 112] 112 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036242 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036242 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036242/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036242 Building REAL250005036243 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036243' /scratch/stefan/7916117/working/building/REAL250005036243 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036243 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036243/0 /scratch/stefan/7916117/working/building/REAL250005036243 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/835 `/scratch/stefan/7916117/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C(F)F)CCCCC1) `REAL250005036243.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036243 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(F)F)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 16, 34, 182, 182, 182, 182, 182, 1, 1, 8, 8, 1, 1, 1, 1, 1, 2, 16, 16, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 20, 21, 22, 23, 24, 25]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036243 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(F)F)CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 15, 15, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 24, 8, 1, 1, 1, 1, 1, 1, 1, 109, 182, 201, 201, 182, 182, 182, 182, 182, 109, 25, 24, 8, 8, 201, 182, 182, 182, 182, 182, 182, 182, 182, 182, 182] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036243 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036243 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036243/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036243 Building REAL250005036244 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036244' /scratch/stefan/7916117/working/building/REAL250005036244 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036244 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036244/0 /scratch/stefan/7916117/working/building/REAL250005036244 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/836 `/scratch/stefan/7916117/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036244.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036244 none CSCC(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 165, 78, 165, 165, 78, 78, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 164, 165, 165, 165, 165, 165, 77, 20, 20, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 895 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036244 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036244 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036244/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036244 Building REAL250005036245 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036245' /scratch/stefan/7916117/working/building/REAL250005036245 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036245 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036245/0 /scratch/stefan/7916117/working/building/REAL250005036245 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/837 `/scratch/stefan/7916117/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCC(F)(F)C1) `REAL250005036245.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036245 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC(F)(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 15, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 67, 102, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 12, 67, 67, 102, 102, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005036245 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC(F)(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 15, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 22, 8, 1, 1, 1, 1, 1, 1, 1, 102, 199, 199, 200, 200, 201, 201, 200, 101, 22, 22, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 646 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036245 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036245 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036245/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036245 Building REAL250005036246 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036246' /scratch/stefan/7916117/working/building/REAL250005036246 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036246 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036246/0 /scratch/stefan/7916117/working/building/REAL250005036246 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/838 `/scratch/stefan/7916117/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Cl)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036246.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036246 none CC1=C(Cl)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 99, 99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 99, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 451 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036246 none CC1=C(Cl)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 60, 88, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 10, 60, 60, 88, 88] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 550 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036246 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036246 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036246/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036246 Building REAL250005036247 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036247' /scratch/stefan/7916117/working/building/REAL250005036247 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036247 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036247/0 /scratch/stefan/7916117/working/building/REAL250005036247 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/839 `/scratch/stefan/7916117/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCOCC1) `REAL250005036247.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036247 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 72, 105, 182, 182, 182, 182, 182, 1, 1, 1, 1, 1, 1, 1, 13, 72, 72, 105, 105, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 182 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 559 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: REAL250005036247 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 12, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 97, 182, 182, 182, 182, 182, 182, 97, 24, 24, 8, 8, 182, 182, 182, 182, 182, 182, 182, 182, 182, 182, 182] 182 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 557 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036247 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036247 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036247/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036247 Building REAL250005036248 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036248' /scratch/stefan/7916117/working/building/REAL250005036248 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036248 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036248/0 /scratch/stefan/7916117/working/building/REAL250005036248 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/840 `/scratch/stefan/7916117/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C2C(=N1)CCCC2C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036248.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036248 none CN1C=C2C(=N1)CCCC2C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 186, 186, 186, 186, 186, 186, 88, 88, 88, 24, 8, 1, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 87, 24, 24, 8, 8] 186 rigid atoms, others: [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]) total number of confs: 564 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: REAL250005036248 none CN1C=C2C(=N1)CCCC2C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 59, 88, 186, 186, 186, 186, 186, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 59, 59, 88, 88] 186 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 520 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036248 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036248 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036248/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036248 Building REAL250005036249 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036249' /scratch/stefan/7916117/working/building/REAL250005036249 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036249 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036249/0 /scratch/stefan/7916117/working/building/REAL250005036249 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/841 `/scratch/stefan/7916117/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(C#N)O1) `REAL250005036249.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036249 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(C#N)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 89, 89, 89, 20, 8, 1, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 189, 189, 189, 189, 88, 21, 21, 8, 8, 189] 189 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 430 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: REAL250005036249 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(C#N)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.1', 'N.1', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 57, 89, 189, 189, 189, 189, 189, 1, 1, 1, 1, 1, 2, 2, 2, 11, 57, 57, 89, 89, 1] 189 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 18, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 537 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036249 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036249 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036249/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036249 Building REAL250005036250 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036250' /scratch/stefan/7916117/working/building/REAL250005036250 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036250 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036250/0 /scratch/stefan/7916117/working/building/REAL250005036250 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/842 `/scratch/stefan/7916117/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC(F)(F)C1)NCCC1=NC(=O)O[N-]1) `REAL250005036250.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036250 none O=C(CC1CCC(F)(F)C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 164, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 164, 164, 201, 201, 201, 201, 201, 201, 201, 49, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036250 none O=C(CC1CCC(F)(F)C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 15, 15, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 113, 114, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 32, 113, 113, 114, 114] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31]) total number of confs: 558 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036250 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036250 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036250/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036250 Building REAL250005036251 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036251' /scratch/stefan/7916117/working/building/REAL250005036251 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036251 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036251/0 /scratch/stefan/7916117/working/building/REAL250005036251 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/843 `/scratch/stefan/7916117/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=CC=CN=C21) `REAL250005036251.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036251 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 1, 12, 12, 65, 101, 182, 182, 182, 182, 182, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 65, 65, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 182 rigid atoms, others: [32, 1, 34, 35, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 552 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: REAL250005036251 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [98, 98, 24, 8, 1, 1, 1, 1, 1, 1, 1, 98, 182, 182, 182, 182, 182, 182, 182, 182, 182, 98, 25, 25, 8, 8, 182, 182, 182, 182, 182, 182, 182, 182, 182, 182] 182 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 555 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036251 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036251 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036251/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036251 Building REAL250005036252 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036252' /scratch/stefan/7916117/working/building/REAL250005036252 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036252 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036252/0 /scratch/stefan/7916117/working/building/REAL250005036252 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/844 `/scratch/stefan/7916117/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1CCOCC1)NCCC1=NC(=O)O[N-]1) `REAL250005036252.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036252 none O=C(CCCC1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 82, 98, 122, 201, 201, 201, 201, 201, 15, 7, 1, 1, 1, 1, 1, 1, 1, 82, 82, 122, 122, 122, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 33, 15, 15, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1001 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036252 none O=C(CCCC1CCOCC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 42, 42, 105, 105, 201, 201, 201, 201, 201, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 105, 105, 105, 105] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036252 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036252 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036252/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036252 Building REAL250005036253 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036253' /scratch/stefan/7916117/working/building/REAL250005036253 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036253 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036253/0 /scratch/stefan/7916117/working/building/REAL250005036253 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/845 `/scratch/stefan/7916117/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C2CCC2)=C1) `REAL250005036253.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036253 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C2CCC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 27, 28, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 8, 8, 8, 1, 5, 27, 27, 28, 28, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1] 201 rigid atoms, others: [1, 36, 11, 12, 13, 14, 15, 16, 20, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) 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: REAL250005036253 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C2CCC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 17, 8, 1, 1, 1, 1, 1, 1, 1, 31, 83, 83, 83, 83, 83, 201, 201, 201, 83, 31, 17, 17, 8, 8, 83, 83, 83, 201, 201, 201, 201, 201, 201, 201, 83] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 566 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: REAL250005036253 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC(C2CCC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 8, 26, 26, 91, 92, 201, 201, 201, 201, 201, 8, 7, 8, 8, 1, 1, 1, 1, 1, 8, 26, 91, 91, 92, 92, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 505 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036253 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036253 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036253/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036253 Building REAL250005036254 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036254' /scratch/stefan/7916117/working/building/REAL250005036254 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036254 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036254/0 /scratch/stefan/7916117/working/building/REAL250005036254 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/846 `/scratch/stefan/7916117/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=C(F)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036254.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036254 none CSC1=C(F)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 143, 143, 143, 143, 143, 143, 143, 68, 68, 68, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 143, 143, 143, 68, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 436 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036254 none CSC1=C(F)C=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 41, 55, 143, 143, 143, 143, 143, 7, 7, 7, 1, 1, 1, 11, 41, 41, 55, 55] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036254 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036254 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036254/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036254 Building REAL250005036255 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036255' /scratch/stefan/7916117/working/building/REAL250005036255 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036255 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036255/0 /scratch/stefan/7916117/working/building/REAL250005036255 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/847 `/scratch/stefan/7916117/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CN(C)N=C1) `REAL250005036255.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036255 none COC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 13, 1, 13, 53, 53, 53, 126, 126, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 26, 26, 26, 13, 53, 126, 126, 126, 126, 1, 2, 2, 2, 1] 201 rigid atoms, others: [33, 2, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 638 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036255 none COC(C(=O)NCCC1=NC(=O)O[N-]1)C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 133, 48, 49, 49, 8, 8, 1, 1, 1, 1, 1, 1, 1, 133, 201, 201, 201, 201, 201, 148, 148, 148, 133, 48, 9, 9, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036255 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036255 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036255/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036255 Building REAL250005036256 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036256' /scratch/stefan/7916117/working/building/REAL250005036256 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036256 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036256/0 /scratch/stefan/7916117/working/building/REAL250005036256 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/848 `/scratch/stefan/7916117/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1C(C)(C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036256.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036256 none CC1=NOC(C)=C1C(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 195, 71, 195, 195, 71, 71, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 195, 195, 195, 195, 195, 195, 71, 19, 19, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 774 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036256 none CC1=NOC(C)=C1C(C)(C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 60, 79, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 15, 60, 60, 79, 79] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 524 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036256 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036256 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036256/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036256 Building REAL250005036257 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036257' /scratch/stefan/7916117/working/building/REAL250005036257 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036257 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036257/0 /scratch/stefan/7916117/working/building/REAL250005036257 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/849 `/scratch/stefan/7916117/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1C) `REAL250005036257.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036257 none CC(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 138, 201, 138, 138, 55, 55, 55, 19, 8, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 201, 201, 201, 138, 55, 19, 19, 8, 8, 138, 138, 138, 138, 138] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 557 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036257 none CC(=O)C1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 11, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 9, 1, 1, 1, 1, 5, 5, 5, 29, 35, 138, 138, 138, 138, 138, 1, 1, 1, 1, 9, 9, 9, 1, 5, 29, 29, 35, 35, 1, 1, 2, 2, 2] 201 rigid atoms, others: [1, 3, 4, 5, 6, 17, 18, 19, 20, 24, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036257 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036257 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036257/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036257 Building REAL250005036258 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036258' /scratch/stefan/7916117/working/building/REAL250005036258 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036258 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036258/0 /scratch/stefan/7916117/working/building/REAL250005036258 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/850 `/scratch/stefan/7916117/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1CC(F)F) `REAL250005036258.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036258 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1CC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 15, 15, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 6, 12, 12, 9, 15, 15, 15, 15, 1, 1, 6, 6, 12] 29 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29]) 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: REAL250005036258 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1CC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 13, 7, 1, 1, 1, 1, 1, 1, 1, 23, 27, 27, 27, 27, 27, 27, 29, 29, 23, 13, 13, 7, 7, 27, 27, 27, 27, 29] 29 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036258 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036258 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036258/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036258 Building REAL250005036259 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036259' /scratch/stefan/7916117/working/building/REAL250005036259 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036259 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036259/0 /scratch/stefan/7916117/working/building/REAL250005036259 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/851 `/scratch/stefan/7916117/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C2CC2)=N1) `REAL250005036259.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036259 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 45, 45, 45, 17, 7, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 201, 201, 117, 117, 117, 117, 45, 17, 17, 7, 7, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 582 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036259 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 9, 9, 9, 39, 40, 117, 117, 117, 117, 117, 1, 1, 1, 13, 13, 1, 2, 2, 2, 9, 39, 39, 40, 40, 13, 13, 13, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036259 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC(C2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 13, 13, 13, 58, 58, 58, 137, 138, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 13, 13, 13, 13, 58, 137, 137, 138, 138, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 610 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036259 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036259 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036259/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036259 Building REAL250005036260 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036260' /scratch/stefan/7916117/working/building/REAL250005036260 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036260 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036260/0 /scratch/stefan/7916117/working/building/REAL250005036260 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/852 `/scratch/stefan/7916117/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC(F)(F)C1) `REAL250005036260.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036260 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 15, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [11, 1, 11, 11, 58, 83, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 11, 58, 58, 83, 83, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 511 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: REAL250005036260 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC(F)(F)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 15, 15, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [101, 101, 23, 8, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 201, 201, 100, 23, 23, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 621 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036260 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036260 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036260/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036260 Building REAL250005036261 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036261' /scratch/stefan/7916117/working/building/REAL250005036261 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036261 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036261/0 /scratch/stefan/7916117/working/building/REAL250005036261 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/853 `/scratch/stefan/7916117/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005036261.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036261 none CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 105, 105, 105, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 25, 25, 8, 8] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 619 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: REAL250005036261 none CC1(C)CCC(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 13, 13, 13, 77, 115, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 13, 77, 77, 115, 115] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 24, 25, 26, 27, 28] set([32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 29, 30, 31]) total number of confs: 636 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036261 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036261 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036261/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036261 Building REAL250005036262 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036262' /scratch/stefan/7916117/working/building/REAL250005036262 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036262 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036262/0 /scratch/stefan/7916117/working/building/REAL250005036262 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/854 `/scratch/stefan/7916117/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005036262.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036262 none CNC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 125, 125, 125, 125, 61, 61, 61, 23, 8, 1, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 125, 125, 60, 23, 23, 8, 8, 125] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 613 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036262 none CNC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [10, 1, 1, 1, 1, 1, 1, 5, 5, 5, 31, 57, 125, 125, 125, 125, 125, 1, 1, 10, 10, 10, 10, 1, 1, 5, 31, 31, 57, 57, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 17, 18, 23, 24, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 368 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036262 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036262 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036262/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036262 Building REAL250005036263 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036263' /scratch/stefan/7916117/working/building/REAL250005036263 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036263 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036263/0 /scratch/stefan/7916117/working/building/REAL250005036263 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/855 `/scratch/stefan/7916117/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CN=C2S1) `REAL250005036263.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036263 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 59, 80, 128, 128, 128, 129, 129, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 58, 58, 81, 81, 1, 1, 1] 129 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036263 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [79, 78, 22, 8, 1, 1, 1, 1, 1, 1, 1, 79, 129, 129, 129, 129, 128, 128, 128, 128, 78, 22, 22, 8, 8, 129, 129, 128] 129 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036263 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036263 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036263/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036263 Building REAL250005036264 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036264' /scratch/stefan/7916117/working/building/REAL250005036264 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036264 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036264/0 /scratch/stefan/7916117/working/building/REAL250005036264 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/856 `/scratch/stefan/7916117/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(CCC(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005036264.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036264 none CC1=CSC(CCC(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 164, 137, 41, 41, 41, 17, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 164, 164, 137, 137, 41, 17, 17, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 774 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036264 none CC1=CSC(CCC(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 7, 13, 59, 60, 60, 128, 129, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 7, 7, 14, 14, 60, 129, 129, 129, 129] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036264 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036264 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036264/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036264 Building REAL250005036265 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036265' /scratch/stefan/7916117/working/building/REAL250005036265 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036265 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036265/0 /scratch/stefan/7916117/working/building/REAL250005036265 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/857 `/scratch/stefan/7916117/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2CCC2)=N1) `REAL250005036265.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036265 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 33, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 13, 13, 13, 1, 6, 25, 25, 33, 33, 1, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036265 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 24, 8, 1, 1, 1, 1, 1, 1, 1, 79, 114, 114, 114, 114, 201, 201, 201, 114, 79, 24, 24, 8, 8, 114, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 607 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036265 none O=C(NCCC1=NC(=O)O[N-]1)C1=COC(C2CCC2)=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 13, 50, 50, 116, 136, 201, 201, 201, 201, 201, 13, 13, 13, 1, 1, 1, 1, 1, 13, 50, 116, 116, 136, 136, 13, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 617 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036265 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036265 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036265/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036265 Building REAL250005036266 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036266' /scratch/stefan/7916117/working/building/REAL250005036266 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036266 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036266/0 /scratch/stefan/7916117/working/building/REAL250005036266 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/858 `/scratch/stefan/7916117/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)N=N1) `REAL250005036266.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036266 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 8, 8, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 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: [12, 1, 12, 12, 69, 88, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 1, 1, 12, 68, 68, 88, 88, 1, 1] 141 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 430 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036266 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(Cl)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 8, 8, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 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: [94, 94, 22, 8, 1, 1, 1, 1, 1, 1, 1, 94, 141, 141, 141, 141, 141, 141, 93, 22, 22, 8, 8, 141, 141] 141 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036266 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036266 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036266/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036266 Building REAL250005036267 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036267' /scratch/stefan/7916117/working/building/REAL250005036267 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036267 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036267/0 /scratch/stefan/7916117/working/building/REAL250005036267 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/859 `/scratch/stefan/7916117/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036267.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036267 none C#CC1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 138, 138, 138, 57, 57, 57, 20, 8, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 56, 20, 20, 8, 8, 138] 138 rigid atoms, others: [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]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036267 none C#CC1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 56, 138, 138, 138, 138, 138, 1, 1, 1, 1, 7, 33, 33, 56, 56, 1] 138 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036267 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036267 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036267/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036267 Building REAL250005036268 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036268' /scratch/stefan/7916117/working/building/REAL250005036268 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036268 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036268/0 /scratch/stefan/7916117/working/building/REAL250005036268 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/860 `/scratch/stefan/7916117/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CN=C1) `REAL250005036268.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036268 none CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 12, 1, 7, 22, 22, 22, 61, 61, 120, 120, 120, 120, 120, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 7, 22, 61, 61, 61, 61, 1, 1, 1, 1] 120 rigid atoms, others: [19, 34, 3, 36, 37, 15, 16, 17, 18, 35, 20] set([0, 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036268 none CC(C)C(C(=O)NCCC1=NC(=O)O[N-]1)C1=CC=CN=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [82, 79, 81, 39, 39, 39, 8, 8, 1, 1, 1, 1, 1, 1, 1, 81, 120, 120, 120, 120, 120, 82, 82, 82, 82, 82, 82, 82, 81, 38, 8, 9, 8, 8, 120, 120, 120, 120] 120 rigid atoms, others: [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, 33, 34, 35, 36, 37]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036268 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036268 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036268/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036268 Building REAL250005036269 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036269' /scratch/stefan/7916117/working/building/REAL250005036269 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036269 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036269/0 /scratch/stefan/7916117/working/building/REAL250005036269 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/861 `/scratch/stefan/7916117/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CO1) `REAL250005036269.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036269 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 185, 185, 85, 85, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 185, 185, 185, 201, 201, 201, 201, 201, 85, 24, 24, 8, 8, 185, 185] 201 rigid atoms, others: [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]) total number of confs: 513 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: REAL250005036269 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [5, 1, 1, 1, 1, 10, 10, 10, 47, 61, 185, 185, 185, 185, 185, 1, 1, 1, 5, 5, 5, 5, 5, 10, 47, 47, 61, 61, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 15, 16, 17, 28, 29] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 423 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036269 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036269 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036269/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036269 Building REAL250005036270 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036270' /scratch/stefan/7916117/working/building/REAL250005036270 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036270 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036270/0 /scratch/stefan/7916117/working/building/REAL250005036270 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/862 `/scratch/stefan/7916117/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)NCCC2=NC(=O)O[N-]2)C1C1=CC=CC=C1) `REAL250005036270.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036270 none CC1C(C(=O)NCCC2=NC(=O)O[N-]2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 93, 93, 93, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 93, 23, 23, 8, 8, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 603 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036270 none CC1C(C(=O)NCCC2=NC(=O)O[N-]2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 71, 99, 201, 201, 201, 201, 201, 1, 1, 2, 2, 1, 2, 2, 2, 2, 2, 1, 1, 13, 71, 71, 99, 99, 1, 2, 2, 1, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 24, 25, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036270 none CC1C(C(=O)NCCC2=NC(=O)O[N-]2)C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 13, 13, 13, 71, 99, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 13, 71, 71, 99, 99, 2, 1, 1, 1, 1, 1] 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]) total number of confs: 568 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036270 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036270 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036270/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036270 Building REAL250005036271 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036271' /scratch/stefan/7916117/working/building/REAL250005036271 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036271 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036271/0 /scratch/stefan/7916117/working/building/REAL250005036271 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/863 `/scratch/stefan/7916117/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN=C1C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036271.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036271 none CC1=CC=CN=C1C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 159, 57, 159, 159, 57, 57, 17, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 57, 17, 17, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 667 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036271 none CC1=CC=CN=C1C(F)(F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 34, 34, 34, 101, 103, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 34, 101, 101, 103, 103] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 557 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036271 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036271 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036271/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036271 Building REAL250005036272 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036272' /scratch/stefan/7916117/working/building/REAL250005036272 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036272 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036272/0 /scratch/stefan/7916117/working/building/REAL250005036272 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/864 `/scratch/stefan/7916117/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036272.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036272 none CSC1=CC=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 150, 150, 150, 115, 150, 150, 150, 66, 66, 66, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 150, 150, 150, 65, 19, 19, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036272 none CSC1=CC=CC(F)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 55, 150, 150, 150, 150, 150, 9, 9, 9, 1, 1, 1, 9, 45, 45, 55, 55] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036272 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036272 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036272/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036272 Building REAL250005036273 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036273' /scratch/stefan/7916117/working/building/REAL250005036273 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036273 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036273/0 /scratch/stefan/7916117/working/building/REAL250005036273 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/865 `/scratch/stefan/7916117/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)NCCC1=NC(=O)O[N-]1)C(F)(F)F) `REAL250005036273.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036273 none CC(C)(CC(=O)NCCC1=NC(=O)O[N-]1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 140, 201, 64, 64, 64, 19, 8, 1, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 142, 142, 64, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 926 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036273 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036273 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036273/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036273 Building REAL250005036274 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036274' /scratch/stefan/7916117/working/building/REAL250005036274 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036274 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036274/0 /scratch/stefan/7916117/working/building/REAL250005036274 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/866 `/scratch/stefan/7916117/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005036274.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036274 none COC(=O)[C@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 103, 201, 103, 103, 103, 103, 44, 103, 44, 44, 19, 9, 1, 1, 1, 1, 1, 1, 1, 103, 103, 201, 201, 201, 103, 103, 103, 103, 44, 19, 19, 9, 9, 103, 103, 103, 103] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL250005036274 none COC(=O)[C@H]1CC[C@H](C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 49, 55, 103, 103, 103, 103, 103, 1, 1, 3, 3, 3, 1, 1, 1, 1, 12, 49, 49, 55, 55, 1, 1, 1, 1] 201 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 10, 38, 21, 22, 36, 26, 27, 28, 29, 37] set([0, 1, 34, 3, 33, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 30, 31]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036274 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036274 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036274/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036274 Building REAL250005036275 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036275' /scratch/stefan/7916117/working/building/REAL250005036275 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036275 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036275/0 /scratch/stefan/7916117/working/building/REAL250005036275 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/867 `/scratch/stefan/7916117/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC1=NC=CN=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036275.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036275 none CCSC1=NC=CN=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 193, 119, 119, 119, 119, 119, 119, 55, 55, 55, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 119, 119, 55, 17, 17, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 439 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036275 none CCSC1=NC=CN=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 35, 39, 119, 119, 119, 119, 119, 28, 28, 28, 28, 28, 1, 1, 9, 35, 35, 39, 39] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036275 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036275 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036275/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036275 Building REAL250005036276 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036276' /scratch/stefan/7916117/working/building/REAL250005036276 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036276 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036276/0 /scratch/stefan/7916117/working/building/REAL250005036276 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/868 `/scratch/stefan/7916117/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NN(CC(F)F)C=C1) `REAL250005036276.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036276 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(CC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 27, 35, 120, 120, 120, 120, 120, 1, 1, 1, 1, 8, 18, 18, 1, 1, 6, 27, 27, 35, 35, 8, 8, 18, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 18, 19, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) 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: REAL250005036276 none O=C(NCCC1=NC(=O)O[N-]1)C1=NN(CC(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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: [81, 81, 24, 8, 1, 1, 1, 1, 1, 1, 1, 81, 120, 120, 120, 187, 201, 201, 120, 120, 81, 24, 24, 8, 8, 187, 187, 201, 120, 120] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 790 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036276 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036276 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036276/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036276 Building REAL250005036277 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036277' /scratch/stefan/7916117/working/building/REAL250005036277 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036277 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036277/0 /scratch/stefan/7916117/working/building/REAL250005036277 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/869 `/scratch/stefan/7916117/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CN=C1F) `REAL250005036277.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036277 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CN=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 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: [12, 1, 12, 12, 72, 103, 186, 186, 186, 186, 186, 1, 1, 1, 1, 1, 1, 1, 12, 72, 72, 103, 103, 1, 1, 1] 186 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) 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: REAL250005036277 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CN=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 15, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 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: [99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 99, 186, 186, 186, 186, 186, 186, 99, 24, 24, 8, 8, 186, 186, 186] 186 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036277 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036277 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036277/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036277 Building REAL250005036278 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036278' /scratch/stefan/7916117/working/building/REAL250005036278 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036278 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036278/0 /scratch/stefan/7916117/working/building/REAL250005036278 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/870 `/scratch/stefan/7916117/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NC=CN1)NCCC1=NC(=O)O[N-]1) `REAL250005036278.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036278 none O=C(CCC1=NC=CN1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 5, 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: [71, 71, 70, 183, 197, 201, 201, 201, 201, 23, 8, 1, 1, 1, 1, 1, 1, 1, 183, 183, 197, 197, 201, 201, 201, 70, 23, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 797 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036278 none O=C(CCC1=NC=CN1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 7, 7, 7, 7, 7, 5, 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: [42, 12, 8, 1, 1, 1, 1, 1, 1, 42, 42, 101, 113, 201, 201, 201, 201, 201, 12, 12, 8, 8, 1, 1, 1, 42, 102, 102, 113, 113] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036278 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036278 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036278/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036278 Building REAL250005036279 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036279' /scratch/stefan/7916117/working/building/REAL250005036279 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036279 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036279/0 /scratch/stefan/7916117/working/building/REAL250005036279 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/871 `/scratch/stefan/7916117/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2NC=CC=C2N=C1) `REAL250005036279.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036279 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2NC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 58, 77, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 58, 58, 77, 77, 1, 1, 1, 1, 1] 151 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 428 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036279 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2NC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [81, 80, 22, 8, 1, 1, 1, 1, 1, 1, 1, 81, 151, 151, 151, 151, 151, 151, 151, 151, 80, 22, 22, 8, 8, 151, 151, 151, 151, 151] 151 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036279 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036279 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036279/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036279 Building REAL250005036280 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036280' /scratch/stefan/7916117/working/building/REAL250005036280 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036280 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036280/0 /scratch/stefan/7916117/working/building/REAL250005036280 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/872 `/scratch/stefan/7916117/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1CCOCC1) `REAL250005036280.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036280 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 13, 13, 13, 58, 78, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 58, 58, 78, 78, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 39, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 513 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: REAL250005036280 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 62, 176, 62, 62, 20, 8, 1, 1, 1, 1, 1, 1, 1, 176, 201, 201, 201, 201, 193, 176, 176, 176, 176, 176, 176, 62, 20, 20, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 841 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036280 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036280 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036280/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036280 Building REAL250005036281 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036281' /scratch/stefan/7916117/working/building/REAL250005036281 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036281 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036281/0 /scratch/stefan/7916117/working/building/REAL250005036281 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/873 `/scratch/stefan/7916117/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1[N+](=O)[O-]) `REAL250005036281.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036281 none NC1=NC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 97, 81, 81, 81, 22, 8, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97, 97, 97, 81, 22, 22, 8, 8] 97 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 283 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036281 none NC1=NC=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 11, 11, 6, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 28, 45, 97, 97, 97, 97, 97, 1, 1, 2, 2, 1, 1, 1, 1, 5, 28, 28, 45, 45] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 21, 22, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 25, 26, 27, 28, 29]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036281 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036281 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036281/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036281 Building REAL250005036282 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036282' /scratch/stefan/7916117/working/building/REAL250005036282 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036282 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036282/0 /scratch/stefan/7916117/working/building/REAL250005036282 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/874 `/scratch/stefan/7916117/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCOC1)NCCC1=NC(=O)O[N-]1) `REAL250005036282.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036282 none O=C(CC1CCCOC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 173, 201, 201, 201, 201, 200, 17, 8, 1, 1, 1, 1, 1, 1, 1, 173, 173, 201, 201, 201, 201, 201, 201, 201, 201, 201, 53, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 770 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036282 none O=C(CC1CCCOC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 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, 10, 1, 1, 1, 1, 1, 1, 1, 31, 31, 103, 105, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 103, 103, 105, 105] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 548 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036282 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036282 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036282/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036282 Building REAL250005036283 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036283' /scratch/stefan/7916117/working/building/REAL250005036283 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036283 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036283/0 /scratch/stefan/7916117/working/building/REAL250005036283 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/875 `/scratch/stefan/7916117/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC2=C1CC(C(=O)NCCC1=NC(=O)O[N-]1)CC2) `REAL250005036283.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036283 none CN1N=CC2=C1CC(C(=O)NCCC1=NC(=O)O[N-]1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 99, 99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 24, 24, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 614 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: REAL250005036283 none CN1N=CC2=C1CC(C(=O)NCCC1=NC(=O)O[N-]1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 12, 12, 12, 67, 102, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 12, 67, 67, 102, 102, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 19, 20, 24, 25, 26, 27, 36, 35] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28, 29, 30, 31]) total number of confs: 593 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036283 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036283 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036283/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036283 Building REAL250005036284 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036284' /scratch/stefan/7916117/working/building/REAL250005036284 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036284 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036284/0 /scratch/stefan/7916117/working/building/REAL250005036284 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/876 `/scratch/stefan/7916117/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@H]1C[C@@H]1C1=CC=CC(F)=C1) `REAL250005036284.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036284 none O=C(NCCC1=NC(=O)O[N-]1)[C@H]1C[C@@H]1C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 58, 60, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 13, 58, 58, 60, 60, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 328 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036284 none O=C(NCCC1=NC(=O)O[N-]1)[C@H]1C[C@@H]1C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 19, 8, 1, 1, 1, 1, 1, 1, 1, 48, 138, 138, 138, 138, 138, 201, 201, 201, 201, 201, 201, 48, 19, 19, 8, 8, 138, 138, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 538 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: REAL250005036284 none O=C(NCCC1=NC(=O)O[N-]1)[C@H]1C[C@@H]1C1=CC=CC(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 31, 31, 103, 105, 201, 201, 201, 201, 201, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 31, 103, 103, 105, 105, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 525 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036284 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036284 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036284/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036284 Building REAL250005036285 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036285' /scratch/stefan/7916117/working/building/REAL250005036285 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036285 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036285/0 /scratch/stefan/7916117/working/building/REAL250005036285 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/877 `/scratch/stefan/7916117/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CN1C) `REAL250005036285.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036285 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 100, 100, 100, 22, 8, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 171, 171, 171, 100, 22, 22, 8, 8, 171, 171, 171, 171, 171] 171 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 400 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: REAL250005036285 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 12, 12, 12, 65, 99, 171, 171, 171, 171, 171, 1, 1, 1, 1, 2, 2, 2, 12, 65, 65, 99, 99, 1, 1, 2, 2, 2] 171 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 17, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 542 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036285 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036285 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036285/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036285 Building REAL250005036286 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036286' /scratch/stefan/7916117/working/building/REAL250005036286 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036286 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036286/0 /scratch/stefan/7916117/working/building/REAL250005036286 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/878 `/scratch/stefan/7916117/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036286.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036286 none CC(C)N1C=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 167, 201, 167, 167, 166, 92, 92, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 167, 201, 201, 201, 201, 201, 201, 201, 167, 92, 24, 24, 8, 8, 167] 201 rigid atoms, others: [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]) total number of confs: 608 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036286 none CC(C)N1C=NC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 7, 37, 48, 168, 168, 168, 168, 168, 1, 13, 13, 13, 12, 12, 12, 12, 1, 8, 36, 36, 48, 48, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 18, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036286 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036286 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036286/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036286 Building REAL250005036287 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036287' /scratch/stefan/7916117/working/building/REAL250005036287 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036287 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036287/0 /scratch/stefan/7916117/working/building/REAL250005036287 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/879 `/scratch/stefan/7916117/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC[NH+](C2CC2)CC1) `REAL250005036287.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036287 none O=C(NCCC1=NC(=O)O[N-]1)C1CC[NH+](C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 67, 88, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 67, 67, 88, 88, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1] 142 rigid atoms, others: [1, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 19, 20, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35]) total number of confs: 443 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036287 none O=C(NCCC1=NC(=O)O[N-]1)C1CC[NH+](C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [78, 78, 17, 8, 1, 1, 1, 1, 1, 1, 1, 78, 142, 142, 142, 142, 142, 142, 142, 142, 142, 78, 17, 17, 8, 8, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142] 142 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036287 none O=C(NCCC1=NC(=O)O[N-]1)C1CC[NH+](C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 3, 20, 20, 77, 94, 142, 142, 142, 142, 142, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 20, 77, 77, 94, 94, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3] 142 rigid atoms, others: [32, 33, 34, 35, 14, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 447 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036287 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036287 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036287/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036287 Building REAL250005036288 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036288' /scratch/stefan/7916117/working/building/REAL250005036288 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036288 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036288/0 /scratch/stefan/7916117/working/building/REAL250005036288 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/880 `/scratch/stefan/7916117/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1Cl) `REAL250005036288.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036288 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 103, 103, 103, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 24, 24, 8, 8] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 461 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036288 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(F)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'F', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 12, 12, 13, 76, 112, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 1, 13, 76, 76, 112, 112] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 25, 26, 27, 28, 29]) total number of confs: 620 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036288 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036288 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036288/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036288 Building REAL250005036289 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036289' /scratch/stefan/7916117/working/building/REAL250005036289 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036289 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036289/0 /scratch/stefan/7916117/working/building/REAL250005036289 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/881 `/scratch/stefan/7916117/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1COCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036289.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036289 none CC1COCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 103, 82, 82, 82, 20, 8, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 103, 82, 21, 20, 8, 8] 103 rigid atoms, others: [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]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036289 none CC1COCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 27, 39, 103, 103, 103, 103, 103, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 27, 27, 39, 39] 103 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036289 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036289 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036289/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036289 Building REAL250005036290 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036290' /scratch/stefan/7916117/working/building/REAL250005036290 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036290 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036290/0 /scratch/stefan/7916117/working/building/REAL250005036290 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/882 `/scratch/stefan/7916117/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC2CCCC(C2)C1) `REAL250005036290.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036290 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2CCCC(C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 1, 13, 13, 74, 104, 191, 191, 191, 191, 191, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 74, 74, 104, 104, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 191 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 567 number of broken/clashed sets: 191 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036290 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2CCCC(C2)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [98, 98, 24, 8, 1, 1, 1, 1, 1, 1, 1, 98, 191, 191, 191, 191, 191, 191, 191, 191, 98, 25, 24, 8, 8, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191, 191] 191 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 590 number of broken/clashed sets: 191 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036290 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036290 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036290/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036290 Building REAL250005036291 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036291' /scratch/stefan/7916117/working/building/REAL250005036291 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036291 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036291/0 /scratch/stefan/7916117/working/building/REAL250005036291 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/883 `/scratch/stefan/7916117/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NS1) `REAL250005036291.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036291 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 83, 83, 83, 22, 8, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 164, 82, 22, 22, 8, 8] 164 rigid atoms, others: [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]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036291 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 71, 100, 164, 164, 164, 164, 164, 1, 1, 2, 2, 2, 1, 13, 71, 71, 100, 100] 164 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 524 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036291 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036291 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036291/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036291 Building REAL250005036292 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036292' /scratch/stefan/7916117/working/building/REAL250005036292 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036292 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036292/0 /scratch/stefan/7916117/working/building/REAL250005036292 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/884 `/scratch/stefan/7916117/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CO1) `REAL250005036292.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036292 none CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 91, 91, 91, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 21, 21, 8, 8, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 445 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: REAL250005036292 none CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [1, 1, 1, 1, 1, 1, 11, 11, 11, 49, 75, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 49, 49, 75, 75, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30]) total number of confs: 502 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036292 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036292 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036292/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036292 Building REAL250005036293 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036293' /scratch/stefan/7916117/working/building/REAL250005036293 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036293 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036293/0 /scratch/stefan/7916117/working/building/REAL250005036293 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/885 `/scratch/stefan/7916117/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036293.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036293 none CCC1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 114, 114, 114, 114, 114, 49, 49, 49, 19, 8, 1, 1, 1, 1, 1, 1, 1, 114, 201, 201, 201, 201, 201, 114, 114, 49, 19, 19, 8, 8, 114] 201 rigid atoms, others: [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]) total number of confs: 794 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036293 none CCC1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 39, 114, 114, 114, 114, 114, 1, 5, 5, 6, 5, 5, 1, 1, 5, 29, 29, 39, 39, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 18, 24, 25, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036293 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036293 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036293/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036293 Building REAL250005036294 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036294' /scratch/stefan/7916117/working/building/REAL250005036294 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036294 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036294/0 /scratch/stefan/7916117/working/building/REAL250005036294 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/886 `/scratch/stefan/7916117/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1=COC=C1) `REAL250005036294.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036294 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1=COC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 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: [11, 1, 11, 12, 45, 47, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 12, 45, 45, 47, 47, 1, 1, 13, 13, 13] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036294 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1=COC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 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: [49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 49, 114, 114, 114, 114, 114, 201, 201, 201, 201, 49, 17, 17, 8, 8, 114, 114, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL250005036294 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1C1=COC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 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: [31, 13, 31, 31, 91, 93, 201, 201, 201, 201, 201, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 31, 91, 91, 93, 93, 13, 13, 1, 1, 1] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 494 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036294 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036294 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036294/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036294 Building REAL250005036295 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036295' /scratch/stefan/7916117/working/building/REAL250005036295 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036295 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036295/0 /scratch/stefan/7916117/working/building/REAL250005036295 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/887 `/scratch/stefan/7916117/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=NC=CN=C2C=C1) `REAL250005036295.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036295 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=NC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 63, 83, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 63, 63, 83, 83, 1, 1, 1, 1] 137 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 428 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036295 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=NC=CN=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 8, 1, 1, 8, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 85, 137, 137, 137, 137, 137, 137, 137, 137, 137, 85, 24, 24, 8, 8, 137, 137, 137, 137] 137 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 353 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036295 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036295 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036295/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036295 Building REAL250005036296 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036296' /scratch/stefan/7916117/working/building/REAL250005036296 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036296 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036296/0 /scratch/stefan/7916117/working/building/REAL250005036296 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/888 `/scratch/stefan/7916117/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1) `REAL250005036296.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036296 none CC1=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 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, 56, 56, 56, 23, 8, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 115, 115, 115, 56, 23, 23, 8, 8, 115, 115] 115 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036296 none CC1=NC2=CC(C(=O)NCCC3=NC(=O)O[N-]3)=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 38, 62, 115, 115, 115, 115, 115, 1, 1, 1, 1, 2, 2, 2, 1, 7, 38, 38, 62, 62, 1, 1] 115 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 24, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036296 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036296 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036296/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036296 Building REAL250005036297 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036297' /scratch/stefan/7916117/working/building/REAL250005036297 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036297 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036297/0 /scratch/stefan/7916117/working/building/REAL250005036297 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/889 `/scratch/stefan/7916117/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2N=N1) `REAL250005036297.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036297 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 53, 65, 124, 124, 124, 125, 125, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 52, 52, 66, 66, 1, 1, 1, 1] 125 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036297 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC2=CC=CC=C2N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 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: [73, 73, 24, 8, 1, 1, 1, 1, 1, 1, 1, 73, 125, 125, 125, 125, 125, 124, 124, 124, 124, 72, 24, 24, 8, 8, 125, 125, 125, 124] 125 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036297 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036297 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036297/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036297 Building REAL250005036298 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036298' /scratch/stefan/7916117/working/building/REAL250005036298 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036298 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036298/0 /scratch/stefan/7916117/working/building/REAL250005036298 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/890 `/scratch/stefan/7916117/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC=C2O1) `REAL250005036298.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036298 none CC1=NC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 186, 93, 93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 186, 186, 186, 93, 24, 24, 8, 8, 186, 186, 186] 186 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036298 none CC1=NC2=C(C(=O)NCCC3=NC(=O)O[N-]3)C=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 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, 12, 12, 12, 61, 85, 186, 186, 186, 186, 186, 1, 1, 1, 1, 1, 2, 2, 2, 13, 61, 61, 85, 85, 1, 1, 1] 186 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036298 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036298 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036298/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036298 Building REAL250005036299 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036299' /scratch/stefan/7916117/working/building/REAL250005036299 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036299 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036299/0 /scratch/stefan/7916117/working/building/REAL250005036299 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/891 `/scratch/stefan/7916117/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C21) `REAL250005036299.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036299 none CN1C=NC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 131, 131, 131, 131, 95, 95, 95, 24, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 131, 131, 95, 24, 24, 8, 8] 131 rigid atoms, others: [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]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036299 none CN1C=NC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 47, 63, 131, 131, 131, 131, 131, 1, 2, 2, 2, 1, 1, 1, 1, 9, 47, 47, 63, 63] 131 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 24, 25, 26, 27] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 31]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036299 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036299 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036299/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036299 Building REAL250005036300 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036300' /scratch/stefan/7916117/working/building/REAL250005036300 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036300 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036300/0 /scratch/stefan/7916117/working/building/REAL250005036300 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/892 `/scratch/stefan/7916117/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CN=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036300.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036300 none COC1=CC=CN=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 200, 200, 200, 200, 200, 200, 166, 55, 55, 55, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 200, 166, 166, 55, 19, 19, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036300 none COC1=CC=CN=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 30, 30, 30, 87, 91, 200, 200, 200, 200, 200, 4, 4, 4, 1, 1, 1, 6, 6, 30, 87, 87, 91, 91] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036300 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036300 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036300/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036300 Building REAL250005036301 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036301' /scratch/stefan/7916117/working/building/REAL250005036301 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036301 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036301/0 /scratch/stefan/7916117/working/building/REAL250005036301 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/893 `/scratch/stefan/7916117/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1) `REAL250005036301.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036301 none CSC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 14, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 168, 83, 83, 83, 23, 8, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 201, 201, 201, 83, 24, 24, 8, 8, 168, 168, 168, 168, 168, 168] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 598 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: REAL250005036301 none CSC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 14, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 11, 11, 11, 51, 70, 168, 168, 168, 168, 168, 1, 1, 1, 7, 7, 7, 11, 51, 51, 70, 70, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 14, 15, 16, 25, 26, 27, 28, 29, 30] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 430 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036301 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036301 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036301/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036301 Building REAL250005036302 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036302' /scratch/stefan/7916117/working/building/REAL250005036302 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036302 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036302/0 /scratch/stefan/7916117/working/building/REAL250005036302 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/894 `/scratch/stefan/7916117/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005036302.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036302 none CC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 119, 127, 119, 119, 119, 71, 71, 71, 19, 8, 1, 1, 1, 1, 1, 1, 1, 119, 127, 127, 127, 119, 119, 71, 19, 19, 8, 8] 127 rigid atoms, others: [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]) total number of confs: 340 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036302 none CC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 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: [8, 1, 8, 1, 1, 1, 1, 1, 10, 10, 10, 48, 61, 119, 119, 119, 119, 119, 1, 9, 9, 9, 1, 1, 10, 48, 48, 61, 61] 127 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 22, 23] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036302 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036302 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036302/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036302 Building REAL250005036303 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036303' /scratch/stefan/7916117/working/building/REAL250005036303 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036303 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036303/0 /scratch/stefan/7916117/working/building/REAL250005036303 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/895 `/scratch/stefan/7916117/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)C2=CC=CC=C21) `REAL250005036303.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036303 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 59, 89, 188, 188, 188, 188, 188, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 59, 59, 89, 89, 1, 1, 1, 1, 1, 1, 1] 188 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 522 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: REAL250005036303 none O=C(NCCC1=NC(=O)O[N-]1)C1CC(=O)C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 23, 8, 1, 1, 1, 1, 1, 1, 1, 85, 188, 188, 188, 188, 188, 188, 188, 188, 188, 85, 24, 24, 8, 8, 188, 188, 188, 188, 188, 188, 188] 188 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 569 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036303 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036303 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036303/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036303 Building REAL250005036304 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036304' /scratch/stefan/7916117/working/building/REAL250005036304 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036304 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036304/0 /scratch/stefan/7916117/working/building/REAL250005036304 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/896 `/scratch/stefan/7916117/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)N(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005036304.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036304 none CC1=CC(=O)N(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 189, 69, 69, 69, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 189, 189, 69, 21, 21, 8, 8, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 698 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036304 none CC1=CC(=O)N(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 4, 28, 28, 28, 102, 114, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 4, 4, 28, 102, 102, 114, 114, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 23, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036304 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036304 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036304/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036304 Building REAL250005036305 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036305' /scratch/stefan/7916117/working/building/REAL250005036305 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036305 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036305/0 /scratch/stefan/7916117/working/building/REAL250005036305 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/897 `/scratch/stefan/7916117/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@@H+]1C1CC1) `REAL250005036305.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036305 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@@H+]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 9, 6, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 1, 7, 7, 32, 45, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 32, 32, 45, 45, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 107 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36]) 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: REAL250005036305 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@@H+]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 9, 6, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [75, 75, 17, 9, 1, 1, 1, 1, 1, 1, 1, 75, 107, 107, 107, 107, 107, 107, 107, 107, 75, 17, 17, 9, 9, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107] 107 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036305 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@@H+]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 9, 6, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 3, 12, 12, 43, 53, 107, 107, 107, 107, 107, 3, 3, 3, 3, 1, 3, 1, 1, 1, 12, 43, 43, 53, 53, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 107 rigid atoms, others: [32, 33, 34, 35, 36, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 302 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036305 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036305/1 /scratch/stefan/7916117/working/building/REAL250005036305 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/898 `/scratch/stefan/7916117/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@H+]1C1CC1) `REAL250005036305.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036305 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@H+]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 9, 6, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 23, 31, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 23, 23, 31, 31, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 71 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36]) 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: REAL250005036305 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@H+]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 9, 6, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 53, 71, 71, 71, 71, 71, 71, 71, 71, 53, 17, 17, 8, 8, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71] 71 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036305 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC[N@H+]1C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 9, 6, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 8, 8, 25, 31, 71, 71, 71, 71, 71, 3, 3, 3, 3, 1, 3, 1, 1, 1, 8, 25, 25, 31, 31, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 71 rigid atoms, others: [32, 33, 34, 35, 36, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 183 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036305 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036305 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036305/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036305/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036305 Building REAL250005036306 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036306' /scratch/stefan/7916117/working/building/REAL250005036306 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036306 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036306/0 /scratch/stefan/7916117/working/building/REAL250005036306 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/899 `/scratch/stefan/7916117/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(Cl)=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036306.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036306 none CC1=CC=CC(Cl)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 151, 201, 201, 201, 201, 201, 169, 43, 43, 43, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 169, 169, 43, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 848 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036306 none CC1=CC=CC(Cl)=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 16, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 20, 89, 95, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 2, 2, 20, 89, 89, 95, 95] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 534 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036306 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036306 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036306/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036306 Building REAL250005036307 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036307' /scratch/stefan/7916117/working/building/REAL250005036307 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036307 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036307/0 /scratch/stefan/7916117/working/building/REAL250005036307 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/900 `/scratch/stefan/7916117/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC(=O)C2=CC=CN21) `REAL250005036307.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036307 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC(=O)C2=CC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 52, 73, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 52, 52, 73, 73, 1, 1, 1, 1, 1, 1, 1, 1] 155 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 426 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036307 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC(=O)C2=CC=CN21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 24, 8, 1, 1, 1, 1, 1, 1, 1, 90, 155, 155, 155, 155, 155, 155, 155, 155, 155, 89, 25, 25, 8, 8, 155, 155, 155, 155, 155, 155, 155, 155] 155 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 482 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036307 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036307 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036307/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036307 Building REAL250005036308 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036308' /scratch/stefan/7916117/working/building/REAL250005036308 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036308 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036308/0 /scratch/stefan/7916117/working/building/REAL250005036308 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/901 `/scratch/stefan/7916117/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CNC(=O)C=C1)NCCC1=NC(=O)O[N-]1) `REAL250005036308.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036308 none O=C(CCC1=CNC(=O)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 11, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [49, 49, 49, 122, 134, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 122, 122, 134, 134, 201, 201, 201, 201, 49, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036308 none O=C(CCC1=CNC(=O)C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 11, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 116, 117, 201, 201, 201, 201, 201, 7, 7, 3, 3, 1, 1, 1, 1, 31, 116, 116, 117, 117] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27] set([0, 1, 2, 32, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036308 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036308 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036308/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036308 Building REAL250005036309 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036309' /scratch/stefan/7916117/working/building/REAL250005036309 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036309 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036309/0 /scratch/stefan/7916117/working/building/REAL250005036309 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/902 `/scratch/stefan/7916117/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(OCC(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005036309.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036309 none CC1CCC(OCC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 185, 126, 43, 43, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 132, 42, 9, 8, 8, 8, 201, 201, 201, 201] 201 rigid atoms, others: [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, 36, 37, 38, 39]) total number of confs: 622 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036309 none CC1CCC(OCC(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 74, 74, 74, 122, 122, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 17, 17, 74, 122, 122, 122, 122, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 18, 19, 23, 24, 25, 26, 27, 28, 37, 36] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 557 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036309 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036309 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036309/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036309 Building REAL250005036310 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036310' /scratch/stefan/7916117/working/building/REAL250005036310 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036310 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036310/0 /scratch/stefan/7916117/working/building/REAL250005036310 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/903 `/scratch/stefan/7916117/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005036310.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036310 none NC(=O)C1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 115, 201, 115, 201, 201, 115, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 115, 115, 49, 17, 17, 8, 8, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 1091 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036310 none NC(=O)C1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 7, 15, 15, 15, 74, 84, 201, 201, 201, 201, 201, 1, 1, 2, 2, 1, 1, 7, 7, 15, 74, 74, 84, 84, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 32, 23, 24, 33] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 518 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036310 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036310 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036310/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036310 Building REAL250005036311 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036311' /scratch/stefan/7916117/working/building/REAL250005036311 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036311 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036311/0 /scratch/stefan/7916117/working/building/REAL250005036311 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/904 `/scratch/stefan/7916117/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005036311.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036311 none CS(=O)(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 35, 37, 37, 27, 27, 27, 13, 7, 1, 1, 1, 1, 1, 1, 1, 35, 35, 37, 37, 37, 27, 13, 13, 7, 7, 35, 35, 35, 35] 37 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL250005036311 none CS(=O)(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [6, 1, 6, 6, 1, 1, 9, 9, 9, 19, 19, 35, 35, 35, 35, 35, 1, 1, 6, 6, 6, 9, 19, 19, 19, 19, 1, 1, 1, 1] 37 rigid atoms, others: [1, 4, 5, 16, 17, 26, 27, 28, 29] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036311 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036311 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036311/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036311 Building REAL250005036312 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036312' /scratch/stefan/7916117/working/building/REAL250005036312 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036312 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036312/0 /scratch/stefan/7916117/working/building/REAL250005036312 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/905 `/scratch/stefan/7916117/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)N1CCOCC1) `REAL250005036312.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036312 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 10, 5, 5, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 83, 101, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 28, 83, 83, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 564 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036312 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 10, 5, 5, 12, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 72, 190, 72, 72, 23, 8, 1, 1, 1, 1, 1, 1, 1, 190, 201, 201, 201, 201, 201, 190, 190, 190, 190, 190, 190, 72, 23, 23, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 776 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036312 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036312 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036312/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036312 Building REAL250005036313 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036313' /scratch/stefan/7916117/working/building/REAL250005036313 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036313 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036313/0 /scratch/stefan/7916117/working/building/REAL250005036313 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/906 `/scratch/stefan/7916117/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(F)CC1CCCCC1) `REAL250005036313.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036313 none O=C(NCCC1=NC(=O)O[N-]1)C(F)CC1CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 12, 49, 49, 109, 113, 201, 201, 201, 201, 201, 5, 12, 1, 1, 1, 1, 1, 1, 1, 49, 109, 109, 113, 113, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036313 none O=C(NCCC1=NC(=O)O[N-]1)C(F)CC1CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 15, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 18, 8, 1, 1, 1, 1, 1, 1, 1, 55, 118, 118, 190, 201, 201, 201, 201, 201, 55, 18, 18, 8, 8, 118, 195, 195, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 907 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036313 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036313 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036313/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036313 Building REAL250005036314 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036314' /scratch/stefan/7916117/working/building/REAL250005036314 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036314 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036314/0 /scratch/stefan/7916117/working/building/REAL250005036314 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/907 `/scratch/stefan/7916117/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC2=CNN=C2C=C1)NCCC1=NC(=O)O[N-]1) `REAL250005036314.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036314 none O=C(CC1=CC2=CNN=C2C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [51, 51, 51, 117, 201, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 201, 201, 201, 51, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 616 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036314 none O=C(CC1=CC2=CNN=C2C=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 69, 79, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 15, 69, 69, 79, 79] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27] set([0, 1, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 504 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036314 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036314 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036314/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036314 Building REAL250005036315 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036315' /scratch/stefan/7916117/working/building/REAL250005036315 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036315 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036315/0 /scratch/stefan/7916117/working/building/REAL250005036315 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/908 `/scratch/stefan/7916117/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(=O)CCC1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036315.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036315 none CC1C(=O)CCC1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 179, 61, 61, 61, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 61, 19, 19, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 780 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036315 none CC1C(=O)CCC1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 1, 6, 27, 27, 27, 106, 111, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 27, 106, 106, 111, 111] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27] set([32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036315 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036315 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036315/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036315 Building REAL250005036316 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036316' /scratch/stefan/7916117/working/building/REAL250005036316 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036316 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036316/0 /scratch/stefan/7916117/working/building/REAL250005036316 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/909 `/scratch/stefan/7916117/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCC(CC(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005036316.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036316 none COC1CCCC(CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 169, 50, 50, 50, 16, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 50, 16, 16, 8, 8, 201, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036316 none COC1CCCC(CC(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 5, 27, 27, 27, 93, 96, 201, 201, 201, 201, 201, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 27, 93, 93, 96, 96, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 38, 39, 19, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 516 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036316 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036316 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036316/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036316 Building REAL250005036317 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036317' /scratch/stefan/7916117/working/building/REAL250005036317 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036317 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036317/0 /scratch/stefan/7916117/working/building/REAL250005036317 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/910 `/scratch/stefan/7916117/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC2=CC=C(F)C=C21) `REAL250005036317.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036317 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2=CC=C(F)C=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 65, 96, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 65, 65, 96, 96, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 562 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: REAL250005036317 none O=C(NCCC1=NC(=O)O[N-]1)C1CC2=CC=C(F)C=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 201, 71, 23, 23, 8, 8, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 560 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036317 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036317 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036317/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036317 Building REAL250005036318 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036318' /scratch/stefan/7916117/working/building/REAL250005036318 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036318 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036318/0 /scratch/stefan/7916117/working/building/REAL250005036318 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/911 `/scratch/stefan/7916117/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)NCCC1=NC(=O)O[N-]1)C1CCCCC1) `REAL250005036318.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036318 none CC(C)(CC(=O)NCCC1=NC(=O)O[N-]1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 37, 37, 37, 98, 98, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 4, 4, 4, 3, 3, 3, 15, 15, 37, 98, 98, 98, 98, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 585 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036318 none CC(C)(CC(=O)NCCC1=NC(=O)O[N-]1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 95, 182, 53, 53, 53, 8, 8, 1, 1, 1, 1, 1, 1, 1, 180, 201, 201, 195, 201, 201, 184, 184, 184, 184, 184, 184, 101, 101, 52, 8, 8, 8, 8, 201, 201, 201, 201, 201, 195, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 838 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036318 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036318 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036318/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036318 Building REAL250005036319 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036319' /scratch/stefan/7916117/working/building/REAL250005036319 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036319 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036319/0 /scratch/stefan/7916117/working/building/REAL250005036319 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/912 `/scratch/stefan/7916117/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(O)=C1F) `REAL250005036319.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036319 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(O)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 12, 1, 15, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 67, 107, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 67, 67, 107, 107, 1, 1, 2] 402 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 27]) total number of confs: 613 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036319 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC(O)=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 12, 1, 15, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 201, 201, 201, 90, 25, 25, 8, 8, 201, 201, 402] 402 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 845 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036319 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036319/1 /scratch/stefan/7916117/working/building/REAL250005036319 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/913 `/scratch/stefan/7916117/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC([O-])=C1F) `REAL250005036319.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036319/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036319 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC([O-])=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 12, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 1, 12, 12, 53, 66, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 53, 53, 66, 66, 1, 1] 112 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) 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: REAL250005036319 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(F)C=CC([O-])=C1F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 12, 1, 15, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [68, 68, 24, 8, 1, 1, 1, 1, 1, 1, 1, 68, 112, 112, 112, 112, 112, 112, 112, 112, 67, 24, 24, 8, 8, 112, 112] 112 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036319 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036319 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036319/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036319/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036319 Building REAL250005036320 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036320' /scratch/stefan/7916117/working/building/REAL250005036320 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036320 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036320/0 /scratch/stefan/7916117/working/building/REAL250005036320 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/914 `/scratch/stefan/7916117/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(F)=CC1CCCCC1) `REAL250005036320.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036320 none O=C(NCCC1=NC(=O)O[N-]1)C(F)=CC1CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'F', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 34, 34, 111, 121, 200, 200, 200, 200, 200, 6, 6, 1, 1, 1, 1, 1, 1, 1, 34, 111, 111, 121, 121, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25]) total number of confs: 571 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036320 none O=C(NCCC1=NC(=O)O[N-]1)C(F)=CC1CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'F', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 15, 1, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 20, 8, 1, 1, 1, 1, 1, 1, 1, 77, 178, 179, 179, 201, 201, 201, 201, 201, 76, 21, 20, 8, 8, 179, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036320 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036320 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036320/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036320 Building REAL250005036321 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036321' /scratch/stefan/7916117/working/building/REAL250005036321 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036321 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036321/0 /scratch/stefan/7916117/working/building/REAL250005036321 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/915 `/scratch/stefan/7916117/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=CC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036321.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036321 none CC(C)CC1=CC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 158, 158, 158, 158, 158, 158, 77, 77, 77, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 158, 158, 158, 76, 21, 21, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL250005036321 none CC(C)CC1=CC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 43, 57, 158, 158, 158, 158, 158, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 43, 43, 57, 57] 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]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036321 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036321 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036321/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036321 Building REAL250005036322 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036322' /scratch/stefan/7916117/working/building/REAL250005036322 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036322 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036322/0 /scratch/stefan/7916117/working/building/REAL250005036322 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/916 `/scratch/stefan/7916117/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C=CCCC2=C1) `REAL250005036322.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036322 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C=CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 1, 7, 7, 40, 60, 116, 116, 116, 116, 116, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 40, 40, 60, 60, 1, 1, 1, 1, 1, 1, 1, 1, 1] 116 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 334 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036322 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2C=CCCC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [52, 52, 22, 8, 1, 1, 1, 1, 1, 1, 1, 52, 116, 116, 115, 116, 116, 116, 116, 116, 116, 51, 22, 22, 8, 8, 116, 116, 116, 116, 116, 116, 116, 116, 116] 116 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036322 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036322 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036322/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036322 Building REAL250005036323 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036323' /scratch/stefan/7916117/working/building/REAL250005036323 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036323 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036323/0 /scratch/stefan/7916117/working/building/REAL250005036323 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/917 `/scratch/stefan/7916117/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=NC(C)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036323.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036323 none CCOC1=NC(C)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 194, 185, 185, 185, 185, 185, 184, 185, 71, 72, 72, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 185, 185, 185, 185, 185, 71, 20, 20, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036323 none CCOC1=NC(C)=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 1, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [17, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 51, 58, 185, 185, 185, 185, 185, 18, 18, 18, 17, 17, 2, 2, 2, 1, 1, 11, 51, 51, 58, 58] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 455 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036323 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036323 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036323/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036323 Building REAL250005036324 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036324' /scratch/stefan/7916117/working/building/REAL250005036324 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036324 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036324/0 /scratch/stefan/7916117/working/building/REAL250005036324 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/918 `/scratch/stefan/7916117/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=CC=C1) `REAL250005036324.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036324 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 7, 31, 31, 95, 104, 201, 201, 201, 201, 201, 1, 7, 1, 1, 1, 1, 1, 1, 31, 95, 95, 104, 104, 1, 1, 1, 1, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23]) 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: REAL250005036324 none O=C(NCCC1=NC(=O)O[N-]1)C(=O)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 19, 8, 1, 1, 1, 1, 1, 1, 1, 73, 158, 158, 201, 201, 194, 201, 201, 73, 19, 19, 8, 8, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 601 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036324 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036324 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036324/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036324 Building REAL250005036325 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036325' /scratch/stefan/7916117/working/building/REAL250005036325 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036325 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036325/0 /scratch/stefan/7916117/working/building/REAL250005036325 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/919 `/scratch/stefan/7916117/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CC(C(F)F)=C1)NCCC1=NC(=O)O[N-]1) `REAL250005036325.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036325 none O=C(CC1=CC=CC(C(F)F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 5, 15, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [36, 36, 36, 36, 40, 40, 36, 40, 40, 47, 47, 40, 16, 8, 1, 1, 1, 1, 1, 1, 1, 36, 36, 40, 40, 36, 47, 40, 36, 16, 16, 8, 8] 47 rigid atoms, others: [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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036325 none O=C(CC1=CC=CC(C(F)F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 5, 15, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [6, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 1, 6, 6, 12, 12, 40, 40, 40, 40, 40, 5, 5, 1, 1, 1, 10, 1, 6, 12, 12, 12, 12] 47 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 11, 23, 24, 25, 27] set([0, 1, 32, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 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/7916117/working/building/REAL250005036325 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036325 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036325/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036325 Building REAL250005036326 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036326' /scratch/stefan/7916117/working/building/REAL250005036326 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036326 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036326/0 /scratch/stefan/7916117/working/building/REAL250005036326 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/920 `/scratch/stefan/7916117/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1) `REAL250005036326.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036326 none CC(C)(C)N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 118, 201, 201, 118, 118, 82, 82, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 81, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 823 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036326 none CC(C)(C)N1C=C(C(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 12, 12, 12, 45, 62, 118, 118, 118, 118, 118, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 12, 45, 45, 62, 62] 201 rigid atoms, others: [1, 4, 5, 6, 7, 18, 19, 29] set([0, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036326 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036326 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036326/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036326 Building REAL250005036327 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036327' /scratch/stefan/7916117/working/building/REAL250005036327 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036327 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036327/0 /scratch/stefan/7916117/working/building/REAL250005036327 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/921 `/scratch/stefan/7916117/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)C=C1Cl) `REAL250005036327.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036327 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 94, 94, 94, 24, 8, 1, 1, 1, 1, 1, 1, 1, 190, 190, 190, 125, 190, 190, 190, 190, 190, 94, 24, 24, 8, 8, 190, 190, 190, 190] 190 rigid atoms, others: [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]) 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: REAL250005036327 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C(C)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 69, 106, 190, 190, 190, 190, 190, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 69, 69, 106, 106, 2, 2, 2, 1] 190 rigid atoms, others: [0, 1, 2, 3, 4, 32, 15, 16, 17, 18, 19, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036327 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036327 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036327/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036327 Building REAL250005036328 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036328' /scratch/stefan/7916117/working/building/REAL250005036328 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036328 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036328/0 /scratch/stefan/7916117/working/building/REAL250005036328 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/922 `/scratch/stefan/7916117/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C#N) `REAL250005036328.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036328 none CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 109, 109, 109, 22, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 108, 22, 22, 8, 8] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 456 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036328 none CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C#N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.1', 'N.1', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 13, 60, 84, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 13, 60, 60, 84, 84] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 26, 27]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036328 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036328 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036328/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036328 Building REAL250005036329 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036329' /scratch/stefan/7916117/working/building/REAL250005036329 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036329 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036329/0 /scratch/stefan/7916117/working/building/REAL250005036329 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/923 `/scratch/stefan/7916117/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1) `REAL250005036329.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036329 none COC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 98, 98, 98, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 98, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 597 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036329 none COC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 11, 11, 11, 55, 74, 201, 201, 201, 201, 201, 1, 1, 1, 1, 6, 6, 6, 11, 55, 55, 74, 74, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 33, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 478 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036329 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036329 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036329/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036329 Building REAL250005036330 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036330' /scratch/stefan/7916117/working/building/REAL250005036330 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036330 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036330/0 /scratch/stefan/7916117/working/building/REAL250005036330 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/924 `/scratch/stefan/7916117/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=CN=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036330.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036330 none COC1=CC(C)=CN=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 175, 175, 175, 175, 175, 174, 174, 84, 84, 84, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 175, 175, 175, 175, 174, 83, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 446 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036330 none COC1=CC(C)=CN=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 61, 70, 175, 175, 175, 174, 174, 4, 4, 4, 1, 2, 2, 2, 1, 12, 61, 61, 71, 71] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 27] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036330 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036330 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036330/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036330 Building REAL250005036331 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036331' /scratch/stefan/7916117/working/building/REAL250005036331 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036331 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036331/0 /scratch/stefan/7916117/working/building/REAL250005036331 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/925 `/scratch/stefan/7916117/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1C1=CC=CC=C1) `REAL250005036331.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036331 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 60, 81, 195, 195, 195, 195, 195, 1, 1, 1, 1, 1, 1, 5, 5, 3, 5, 5, 12, 60, 60, 81, 81, 1, 1, 5, 5, 3, 5, 5] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 504 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036331 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 8, 1, 1, 1, 1, 1, 1, 1, 68, 195, 195, 195, 195, 195, 201, 201, 201, 201, 201, 68, 23, 23, 8, 8, 195, 195, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036331 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 80, 99, 201, 201, 201, 201, 201, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 19, 80, 80, 99, 99, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 542 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036331 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036331 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036331/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036331 Building REAL250005036332 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036332' /scratch/stefan/7916117/working/building/REAL250005036332 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036332 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036332/0 /scratch/stefan/7916117/working/building/REAL250005036332 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/926 `/scratch/stefan/7916117/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)CCC(=O)NCCC2=NC(=O)O[N-]2)C=N1) `REAL250005036332.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036332 none CN1C=C(C(=O)CCC(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [196, 195, 193, 146, 127, 146, 92, 36, 36, 36, 8, 8, 1, 1, 1, 1, 1, 1, 1, 195, 195, 195, 198, 197, 193, 133, 133, 105, 105, 35, 9, 8, 8, 8, 195] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 747 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036332 none CN1C=C(C(=O)CCC(=O)NCCC2=NC(=O)O[N-]2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 20, 24, 59, 59, 59, 107, 107, 193, 192, 195, 192, 192, 1, 1, 2, 2, 2, 1, 20, 20, 24, 24, 59, 112, 112, 112, 112, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 34, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036332 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036332 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036332/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036332 Building REAL250005036333 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036333' /scratch/stefan/7916117/working/building/REAL250005036333 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036333 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036333/0 /scratch/stefan/7916117/working/building/REAL250005036333 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/927 `/scratch/stefan/7916117/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(OC)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036333.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036333 none CCC(C)C(OC)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 130, 184, 53, 135, 155, 53, 53, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 201, 183, 186, 186, 186, 135, 155, 155, 155, 52, 9, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 904 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036333 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036333 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036333/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036333 Building REAL250005036334 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036334' /scratch/stefan/7916117/working/building/REAL250005036334 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036334 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036334/0 /scratch/stefan/7916117/working/building/REAL250005036334 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/928 `/scratch/stefan/7916117/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=NC=C(Cl)S1) `REAL250005036334.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036334 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC=C(Cl)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [13, 1, 13, 13, 63, 82, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 1, 13, 63, 63, 82, 82, 1] 134 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) 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: REAL250005036334 none O=C(NCCC1=NC(=O)O[N-]1)C1=NC=C(Cl)S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [75, 75, 23, 8, 1, 1, 1, 1, 1, 1, 1, 75, 134, 134, 134, 134, 134, 74, 23, 23, 8, 8, 134] 134 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036334 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036334 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036334/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036334 Building REAL250005036335 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036335' /scratch/stefan/7916117/working/building/REAL250005036335 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036335 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036335/0 /scratch/stefan/7916117/working/building/REAL250005036335 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/929 `/scratch/stefan/7916117/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCCC1=NC(=O)O[N-]1)C(=O)OC) `REAL250005036335.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036335 none CCC(C(=O)NCCC1=NC(=O)O[N-]1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 5, 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: [164, 141, 49, 49, 49, 17, 8, 1, 1, 1, 1, 1, 1, 1, 141, 180, 180, 180, 164, 164, 164, 164, 164, 141, 49, 17, 17, 8, 8, 180, 180, 180] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 838 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036335 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036335 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036335/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036335 Building REAL250005036336 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036336' /scratch/stefan/7916117/working/building/REAL250005036336 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036336 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036336/0 /scratch/stefan/7916117/working/building/REAL250005036336 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/930 `/scratch/stefan/7916117/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)CCCO1) `REAL250005036336.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036336 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 184, 184, 93, 93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 201, 201, 201, 201, 201, 93, 24, 24, 8, 8, 184, 184, 184, 184, 184, 184] 201 rigid atoms, others: [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, 33, 34]) total number of confs: 542 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036336 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 9, 9, 9, 38, 54, 184, 184, 184, 184, 184, 1, 1, 1, 1, 4, 4, 4, 4, 4, 9, 38, 38, 54, 54, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 33, 34, 15, 16, 17, 18, 29, 30, 31] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036336 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036336 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036336/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036336 Building REAL250005036337 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036337' /scratch/stefan/7916117/working/building/REAL250005036337 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036337 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036337/0 /scratch/stefan/7916117/working/building/REAL250005036337 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/931 `/scratch/stefan/7916117/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036337.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036337 none CC(C)(C)OC(=O)CCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 122, 201, 99, 41, 41, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124, 103, 103, 40, 9, 8, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 714 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036337 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036337 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036337/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036337 Building REAL250005036338 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036338' /scratch/stefan/7916117/working/building/REAL250005036338 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036338 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036338/0 /scratch/stefan/7916117/working/building/REAL250005036338 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/932 `/scratch/stefan/7916117/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1(CC(=O)NCCC2=NC(=O)O[N-]2)CCC1) `REAL250005036338.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036338 none CCOC(=O)C1(CC(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 7, 3, 7, 5, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 176, 175, 141, 175, 111, 57, 57, 57, 20, 8, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 201, 201, 201, 201, 201, 114, 114, 56, 20, 20, 8, 8, 141, 141, 141, 141, 141, 141] 201 rigid atoms, others: [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, 36, 37, 38]) total number of confs: 867 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036338 none CCOC(=O)C1(CC(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 7, 3, 7, 5, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 6, 1, 6, 1, 1, 5, 13, 13, 13, 41, 49, 141, 141, 141, 141, 141, 1, 1, 1, 20, 20, 20, 20, 20, 5, 5, 13, 41, 41, 49, 49, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 3, 36, 5, 6, 18, 19, 20, 38, 37, 35] set([0, 1, 2, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036338 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036338 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036338/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036338 Building REAL250005036339 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036339' /scratch/stefan/7916117/working/building/REAL250005036339 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036339 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036339/0 /scratch/stefan/7916117/working/building/REAL250005036339 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/933 `/scratch/stefan/7916117/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCC1=NC(=O)O[N-]1)N(C)CC(F)(F)F) `REAL250005036339.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036339 none CC(C(=O)NCCC1=NC(=O)O[N-]1)N(C)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 10, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 67, 67, 67, 19, 8, 1, 1, 1, 1, 1, 1, 1, 155, 180, 180, 201, 201, 201, 201, 155, 155, 155, 155, 67, 19, 19, 8, 8, 180, 180, 180, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 828 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036339 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036339 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036339/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036339 Building REAL250005036340 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036340' /scratch/stefan/7916117/working/building/REAL250005036340 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036340 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036340/0 /scratch/stefan/7916117/working/building/REAL250005036340 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/934 `/scratch/stefan/7916117/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005036340.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036340 none COC1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 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, 103, 71, 71, 71, 24, 8, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 103, 103, 71, 24, 24, 8, 8] 103 rigid atoms, others: [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]) 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: REAL250005036340 none COC1=CN=CC(C(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 39, 49, 103, 103, 103, 103, 103, 1, 2, 2, 2, 1, 1, 11, 39, 39, 49, 49] 103 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 22, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036340 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036340 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036340/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036340 Building REAL250005036341 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036341' /scratch/stefan/7916117/working/building/REAL250005036341 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036341 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036341/0 /scratch/stefan/7916117/working/building/REAL250005036341 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/935 `/scratch/stefan/7916117/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1Cl) `REAL250005036341.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036341 none CC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 169, 127, 34, 34, 34, 18, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127, 34, 18, 18, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036341 none CC1=CC=CC(CC(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 6, 35, 35, 35, 118, 118, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 6, 6, 35, 118, 118, 118, 118] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 23, 24, 25] set([32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036341 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036341 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036341/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036341 Building REAL250005036342 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036342' /scratch/stefan/7916117/working/building/REAL250005036342 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036342 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036342/0 /scratch/stefan/7916117/working/building/REAL250005036342 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/936 `/scratch/stefan/7916117/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C2CCCCN12) `REAL250005036342.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036342 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C2CCCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 1, 13, 13, 59, 80, 172, 172, 172, 172, 172, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 59, 59, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 1] 172 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 463 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: REAL250005036342 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN=C2CCCCN12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [86, 85, 24, 8, 1, 1, 1, 1, 1, 1, 1, 86, 172, 172, 172, 172, 172, 172, 172, 172, 85, 24, 24, 8, 8, 172, 172, 172, 172, 172, 172, 172, 172, 172] 172 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 398 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036342 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036342 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036342/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036342 Building REAL250005036343 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036343' /scratch/stefan/7916117/working/building/REAL250005036343 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036343 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036343/0 /scratch/stefan/7916117/working/building/REAL250005036343 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/937 `/scratch/stefan/7916117/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1[N+](=O)[O-]) `REAL250005036343.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036343 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 8, 11, 11, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 48, 68, 156, 156, 156, 156, 156, 1, 1, 1, 1, 1, 1, 1, 1, 9, 48, 48, 68, 68, 1, 1] 156 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036343 none O=C(NCCC1=NC(=O)O[N-]1)C1=CNN=C1[N+](=O)[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 8, 1, 8, 11, 11, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 24, 8, 1, 1, 1, 1, 1, 1, 1, 92, 156, 156, 156, 156, 156, 155, 156, 92, 24, 24, 8, 8, 156, 156] 156 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036343 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036343 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036343/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036343 Building REAL250005036344 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036344' /scratch/stefan/7916117/working/building/REAL250005036344 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036344 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036344/0 /scratch/stefan/7916117/working/building/REAL250005036344 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/938 `/scratch/stefan/7916117/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005036344.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036344 none CN(C)C(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 179, 201, 75, 75, 75, 19, 8, 1, 1, 1, 1, 1, 1, 1, 179, 179, 201, 201, 201, 201, 201, 201, 75, 19, 19, 8, 8, 179, 179, 179, 179] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 636 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036344 none CN(C)C(=O)C1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 4, 5, 1, 4, 1, 1, 7, 7, 7, 44, 64, 179, 179, 179, 179, 179, 1, 1, 5, 5, 5, 5, 5, 5, 7, 44, 44, 64, 64, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 3, 5, 6, 17, 18, 30, 31] set([0, 1, 2, 4, 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: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036344 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036344 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036344/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036344 Building REAL250005036345 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036345' /scratch/stefan/7916117/working/building/REAL250005036345 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036345 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036345/0 /scratch/stefan/7916117/working/building/REAL250005036345 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/939 `/scratch/stefan/7916117/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1) `REAL250005036345.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036345 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 91, 91, 91, 24, 8, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 139, 139, 139, 139, 91, 25, 25, 8, 8, 139] 139 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036345 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 43, 67, 139, 139, 139, 139, 139, 1, 1, 1, 2, 2, 2, 1, 1, 7, 43, 43, 67, 67, 1] 139 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 22, 23, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036345 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036345 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036345/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036345 Building REAL250005036346 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036346' /scratch/stefan/7916117/working/building/REAL250005036346 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036346 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036346/0 /scratch/stefan/7916117/working/building/REAL250005036346 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/940 `/scratch/stefan/7916117/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NOC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036346.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036346 none COCC1=NOC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 183, 126, 126, 126, 126, 126, 57, 57, 57, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 183, 183, 126, 57, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036346 none COCC1=NOC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 35, 43, 126, 126, 126, 126, 126, 30, 30, 30, 8, 8, 1, 7, 35, 35, 43, 43] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 24] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036346 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036346 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036346/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036346 Building REAL250005036347 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036347' /scratch/stefan/7916117/working/building/REAL250005036347 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036347 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036347/0 /scratch/stefan/7916117/working/building/REAL250005036347 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/941 `/scratch/stefan/7916117/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC=C1C(=O)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036347.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036347 none CN1C=CC=C1C(=O)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 169, 69, 169, 69, 69, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 69, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036347 none CN1C=CC=C1C(=O)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 35, 35, 35, 114, 121, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 35, 114, 114, 121, 121] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036347 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036347 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036347/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036347 Building REAL250005036348 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036348' /scratch/stefan/7916117/working/building/REAL250005036348 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036348 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036348/0 /scratch/stefan/7916117/working/building/REAL250005036348 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/942 `/scratch/stefan/7916117/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2OC(=O)NC2=C1) `REAL250005036348.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036348 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2OC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 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, 7, 37, 61, 118, 118, 118, 118, 118, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 61, 61, 1, 1, 1, 1] 118 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036348 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2OC(=O)NC2=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 1, 11, 8, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 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: [58, 58, 21, 8, 1, 1, 1, 1, 1, 1, 1, 58, 118, 118, 118, 118, 118, 118, 118, 118, 118, 57, 21, 21, 8, 8, 118, 118, 118, 118] 118 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036348 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036348 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036348/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036348 Building REAL250005036349 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036349' /scratch/stefan/7916117/working/building/REAL250005036349 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036349 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036349/0 /scratch/stefan/7916117/working/building/REAL250005036349 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/943 `/scratch/stefan/7916117/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2CCCC2=CO1) `REAL250005036349.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036349 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2CCCC2=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 13, 55, 74, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 1, 1, 13, 55, 55, 74, 74, 1, 1, 1, 1, 1, 1, 1] 160 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 431 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036349 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2CCCC2=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 83, 160, 160, 160, 160, 160, 160, 160, 82, 24, 24, 8, 8, 160, 160, 160, 160, 160, 160, 160] 160 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036349 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036349 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036349/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036349 Building REAL250005036350 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036350' /scratch/stefan/7916117/working/building/REAL250005036350 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036350 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036350/0 /scratch/stefan/7916117/working/building/REAL250005036350 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/944 `/scratch/stefan/7916117/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1) `REAL250005036350.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036350 none CCOC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 198, 102, 102, 102, 24, 8, 1, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 201, 201, 201, 201, 201, 102, 24, 24, 8, 8, 198, 198, 198, 198, 198, 198, 198, 198] 201 rigid atoms, others: [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, 33, 34, 35, 36]) total number of confs: 601 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: REAL250005036350 none CCOC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 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, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 9, 9, 9, 49, 77, 198, 198, 198, 198, 198, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 49, 49, 77, 77, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 34, 15, 16, 17, 18, 35, 36, 29, 30, 31] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 513 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036350 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036350 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036350/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036350 Building REAL250005036351 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036351' /scratch/stefan/7916117/working/building/REAL250005036351 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036351 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036351/0 /scratch/stefan/7916117/working/building/REAL250005036351 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/945 `/scratch/stefan/7916117/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2CCOCC2=CO1) `REAL250005036351.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036351 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2CCOCC2=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 12, 5, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 62, 92, 177, 177, 177, 177, 177, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 62, 62, 92, 92, 1, 1, 1, 1, 1, 1, 1] 177 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 511 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: REAL250005036351 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2CCOCC2=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 12, 5, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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: [93, 93, 22, 8, 1, 1, 1, 1, 1, 1, 1, 93, 177, 177, 177, 177, 177, 176, 177, 177, 92, 22, 22, 8, 8, 177, 177, 177, 177, 177, 177, 177] 177 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 406 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036351 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036351 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036351/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036351 Building REAL250005036352 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036352' /scratch/stefan/7916117/working/building/REAL250005036352 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036352 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036352/0 /scratch/stefan/7916117/working/building/REAL250005036352 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/946 `/scratch/stefan/7916117/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1OCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036352.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036352 none CCC1OCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 82, 59, 59, 59, 20, 8, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 82, 59, 20, 20, 8, 8] 82 rigid atoms, others: [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]) total number of confs: 293 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: REAL250005036352 none CCC1OCCC1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 1, 1, 1, 1, 1, 1, 4, 4, 4, 18, 29, 82, 82, 82, 82, 82, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 18, 18, 29, 29] 82 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 23, 24, 25, 26, 27, 28] set([0, 32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 205 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036352 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036352 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036352/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036352 Building REAL250005036353 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036353' /scratch/stefan/7916117/working/building/REAL250005036353 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036353 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036353/0 /scratch/stefan/7916117/working/building/REAL250005036353 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/947 `/scratch/stefan/7916117/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=C(COCC(=O)NCCC2=NC(=O)O[N-]2)O1) `REAL250005036353.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036353 none CC1=CN=C(COCC(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 152, 92, 71, 30, 30, 30, 7, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 152, 152, 80, 80, 29, 8, 7, 7, 7] 201 rigid atoms, others: [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]) total number of confs: 698 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036353 none CC1=CN=C(COCC(=O)NCCC2=NC(=O)O[N-]2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 26, 56, 62, 62, 62, 122, 122, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 8, 8, 56, 56, 62, 122, 122, 122, 122] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036353 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036353 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036353/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036353 Building REAL250005036354 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036354' /scratch/stefan/7916117/working/building/REAL250005036354 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036354 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036354/0 /scratch/stefan/7916117/working/building/REAL250005036354 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/948 `/scratch/stefan/7916117/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005036354.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036354 none COCC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 183, 99, 99, 99, 99, 59, 59, 59, 19, 8, 1, 1, 1, 1, 1, 1, 1, 99, 201, 201, 201, 183, 183, 99, 59, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 713 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036354 none COCC1=NC=C(C(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [19, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 27, 33, 99, 99, 99, 99, 99, 1, 20, 19, 19, 5, 5, 1, 6, 27, 27, 33, 33] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 18, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036354 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036354 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036354/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036354 Building REAL250005036355 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036355' /scratch/stefan/7916117/working/building/REAL250005036355 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036355 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036355/0 /scratch/stefan/7916117/working/building/REAL250005036355 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/949 `/scratch/stefan/7916117/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CN1) `REAL250005036355.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036355 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 154, 154, 76, 76, 77, 24, 8, 1, 1, 1, 1, 1, 1, 1, 154, 154, 154, 201, 201, 201, 201, 201, 76, 24, 24, 8, 8, 154, 154, 154] 201 rigid atoms, others: [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]) total number of confs: 646 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: REAL250005036355 none CCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 11, 11, 11, 53, 65, 154, 154, 154, 154, 154, 1, 1, 1, 6, 6, 6, 6, 6, 11, 53, 53, 65, 65, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 15, 16, 17, 28, 29, 30] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 394 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036355 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036355 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036355/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036355 Building REAL250005036356 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036356' /scratch/stefan/7916117/working/building/REAL250005036356 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036356 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036356/0 /scratch/stefan/7916117/working/building/REAL250005036356 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/950 `/scratch/stefan/7916117/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CN1) `REAL250005036356.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036356 none CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 90, 90, 90, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 21, 21, 8, 8, 201, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 447 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: REAL250005036356 none CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 49, 75, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 11, 49, 49, 75, 75, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 16, 17, 18, 22, 33, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 512 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036356 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036356 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036356/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036356 Building REAL250005036357 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036357' /scratch/stefan/7916117/working/building/REAL250005036357 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036357 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036357/0 /scratch/stefan/7916117/working/building/REAL250005036357 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/951 `/scratch/stefan/7916117/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C(C(C)C)O1) `REAL250005036357.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036357 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C(C(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 77, 77, 77, 22, 8, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 201, 201, 148, 148, 148, 148, 76, 22, 22, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL250005036357 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)N=C(C(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 33, 46, 148, 148, 148, 148, 148, 1, 1, 1, 13, 13, 1, 2, 2, 2, 7, 33, 33, 46, 46, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036357 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036357 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036357/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036357 Building REAL250005036358 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036358' /scratch/stefan/7916117/working/building/REAL250005036358 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036358 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036358/0 /scratch/stefan/7916117/working/building/REAL250005036358 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/952 `/scratch/stefan/7916117/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036358.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036358 none CC(C)(C)CCCCC(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 163, 193, 195, 201, 140, 152, 51, 51, 51, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 195, 201, 193, 201, 201, 201, 195, 201, 201, 200, 199, 178, 178, 152, 152, 51, 17, 17, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036358 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036358 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036358/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036358 Building REAL250005036359 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036359' /scratch/stefan/7916117/working/building/REAL250005036359 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036359 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036359/0 /scratch/stefan/7916117/working/building/REAL250005036359 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/953 `/scratch/stefan/7916117/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C12) `REAL250005036359.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036359 none CC1=CC=NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 117, 117, 117, 117, 62, 62, 62, 24, 8, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 117, 117, 117, 117, 61, 24, 24, 8, 8, 117] 117 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036359 none CC1=CC=NC2=CC=C(C(=O)NCCC3=NC(=O)O[N-]3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 33, 53, 117, 117, 117, 117, 117, 1, 1, 2, 2, 2, 1, 1, 1, 1, 6, 33, 33, 53, 53, 1] 117 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 20, 21, 25, 26, 27, 28] set([32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 29, 30, 31]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036359 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036359 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036359/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036359 Building REAL250005036360 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036360' /scratch/stefan/7916117/working/building/REAL250005036360 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036360 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036360/0 /scratch/stefan/7916117/working/building/REAL250005036360 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/954 `/scratch/stefan/7916117/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(COCC(=O)NCCC2=NC(=O)O[N-]2)S1) `REAL250005036360.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036360 none CC1=NN=C(COCC(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 187, 129, 95, 32, 32, 32, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 187, 187, 103, 103, 32, 8, 8, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 755 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036360 none CC1=NN=C(COCC(=O)NCCC2=NC(=O)O[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 22, 58, 80, 80, 80, 138, 138, 201, 201, 201, 201, 201, 1, 2, 2, 2, 8, 8, 58, 58, 80, 138, 138, 138, 138] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 679 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036360 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036360 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036360/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036360 Building REAL250005036361 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036361' /scratch/stefan/7916117/working/building/REAL250005036361 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036361 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036361/0 /scratch/stefan/7916117/working/building/REAL250005036361 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/955 `/scratch/stefan/7916117/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC(C)(C)CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036361.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036361 none CCOC(=O)CC(C)(C)CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 17, 17, 7, 17, 7, 7, 7, 7, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5] 19 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036361 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036361 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036361/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036361 Building REAL250005036362 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036362' /scratch/stefan/7916117/working/building/REAL250005036362 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036362 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036362/0 /scratch/stefan/7916117/working/building/REAL250005036362 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/956 `/scratch/stefan/7916117/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OCCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036362.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036362 none CC(C)(C)OCCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 156, 164, 46, 46, 46, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 198, 198, 164, 164, 46, 17, 17, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1018 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036362 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036362 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036362/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036362 Building REAL250005036363 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036363' /scratch/stefan/7916117/working/building/REAL250005036363 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036363 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036363/0 /scratch/stefan/7916117/working/building/REAL250005036363 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/957 `/scratch/stefan/7916117/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1) `REAL250005036363.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036363 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 52, 52, 52, 24, 8, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 116, 51, 24, 24, 8, 8, 116] 116 rigid atoms, others: [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]) total number of confs: 288 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036363 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 33, 57, 116, 116, 116, 116, 116, 1, 1, 2, 2, 2, 1, 5, 33, 33, 57, 57, 1] 116 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 20, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 21, 22, 23, 24, 25]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036363 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036363 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036363/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036363 Building REAL250005036364 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036364' /scratch/stefan/7916117/working/building/REAL250005036364 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036364 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036364/0 /scratch/stefan/7916117/working/building/REAL250005036364 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/958 `/scratch/stefan/7916117/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=NN1) `REAL250005036364.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036364 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 8, 8, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 4, 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: [13, 1, 13, 13, 62, 78, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 1, 1, 13, 62, 62, 78, 78, 1, 1] 135 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) total number of confs: 391 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036364 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 8, 8, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 4, 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: [79, 79, 24, 8, 1, 1, 1, 1, 1, 1, 1, 79, 135, 135, 135, 135, 135, 135, 135, 79, 24, 24, 8, 8, 135, 135] 135 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036364 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036364 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036364/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036364 Building REAL250005036365 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036365' /scratch/stefan/7916117/working/building/REAL250005036365 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036365 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036365/0 /scratch/stefan/7916117/working/building/REAL250005036365 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/959 `/scratch/stefan/7916117/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)N=C1) `REAL250005036365.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036365 none COC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 164, 164, 164, 164, 104, 29, 29, 29, 13, 7, 1, 1, 1, 1, 1, 1, 1, 164, 164, 201, 201, 201, 164, 164, 104, 104, 29, 13, 13, 7, 7, 164] 201 rigid atoms, others: [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]) total number of confs: 561 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036365 none COC1=CC=C(CC(=O)NCCC2=NC(=O)O[N-]2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 1, 1, 1, 5, 28, 28, 28, 93, 94, 164, 164, 164, 164, 164, 1, 1, 3, 3, 3, 1, 1, 5, 5, 28, 93, 93, 94, 94, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 18, 19, 23, 24] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036365 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036365 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036365/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036365 Building REAL250005036366 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036366' /scratch/stefan/7916117/working/building/REAL250005036366 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036366 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036366/0 /scratch/stefan/7916117/working/building/REAL250005036366 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/960 `/scratch/stefan/7916117/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(C(C)C)O1) `REAL250005036366.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036366 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(C(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 68, 68, 68, 19, 8, 1, 1, 1, 1, 1, 1, 1, 169, 169, 169, 201, 201, 169, 169, 169, 169, 68, 20, 20, 8, 8, 169, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL250005036366 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C(C(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 49, 62, 169, 169, 169, 169, 169, 1, 1, 1, 4, 4, 1, 2, 2, 2, 7, 49, 49, 62, 62, 1, 4, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 19, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036366 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036366 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036366/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036366 Building REAL250005036367 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036367' /scratch/stefan/7916117/working/building/REAL250005036367 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036367 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036367/0 /scratch/stefan/7916117/working/building/REAL250005036367 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/961 `/scratch/stefan/7916117/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CCCCCC1) `REAL250005036367.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036367 none O=C(NCCC1=NC(=O)O[N-]1)C1=CCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 74, 112, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 12, 74, 74, 112, 112, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) total number of confs: 603 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: REAL250005036367 none O=C(NCCC1=NC(=O)O[N-]1)C1=CCCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 24, 8, 1, 1, 1, 1, 1, 1, 1, 99, 201, 201, 201, 201, 201, 201, 99, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 447 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036367 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036367 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036367/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036367 Building REAL250005036368 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036368' /scratch/stefan/7916117/working/building/REAL250005036368 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036368 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036368/0 /scratch/stefan/7916117/working/building/REAL250005036368 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/962 `/scratch/stefan/7916117/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC1=NC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036368.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036368 none CC(C)OC1=NC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 181, 181, 181, 181, 181, 181, 64, 64, 64, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 64, 23, 23, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036368 none CC(C)OC1=NC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [17, 5, 17, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 57, 181, 181, 181, 181, 181, 18, 18, 18, 17, 17, 17, 17, 1, 1, 1, 12, 50, 50, 57, 57] 201 rigid atoms, others: [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, 34, 35]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036368 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036368 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036368/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036368 Building REAL250005036369 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036369' /scratch/stefan/7916117/working/building/REAL250005036369 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036369 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036369/0 /scratch/stefan/7916117/working/building/REAL250005036369 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/963 `/scratch/stefan/7916117/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(Cl)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036369.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036369 none N#CC1=CC=C(Cl)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 177, 177, 177, 177, 88, 88, 88, 23, 8, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 88, 23, 23, 8, 8, 177] 177 rigid atoms, others: [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]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036369 none N#CC1=CC=C(Cl)C(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 16, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 63, 177, 177, 177, 177, 177, 1, 1, 1, 7, 39, 39, 63, 63, 1] 177 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26]) total number of confs: 441 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036369 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036369 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036369/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036369 Building REAL250005036370 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036370' /scratch/stefan/7916117/working/building/REAL250005036370 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036370 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036370/0 /scratch/stefan/7916117/working/building/REAL250005036370 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/964 `/scratch/stefan/7916117/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2CCCCC21) `REAL250005036370.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036370 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2CCCCC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 1, 8, 8, 42, 58, 129, 129, 129, 129, 129, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 42, 42, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 129 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 345 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036370 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCC2CCCCC21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 76, 129, 129, 129, 129, 129, 129, 129, 129, 129, 75, 24, 24, 8, 8, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129] 129 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036370 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036370 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036370/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036370 Building REAL250005036371 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036371' /scratch/stefan/7916117/working/building/REAL250005036371 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036371 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036371/0 /scratch/stefan/7916117/working/building/REAL250005036371 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/965 `/scratch/stefan/7916117/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C) `REAL250005036371.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036371 none CC1=COC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 178, 178, 105, 105, 105, 24, 8, 1, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 179, 178, 104, 24, 24, 8, 8, 179, 179, 179] 179 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 424 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: REAL250005036371 none CC1=COC(C(=O)NCCC2=NC(=O)O[N-]2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 11, 67, 112, 178, 178, 178, 179, 179, 1, 1, 2, 2, 2, 1, 11, 66, 66, 112, 112, 2, 2, 2] 179 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 21] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 598 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036371 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036371 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036371/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036371 Building REAL250005036372 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036372' /scratch/stefan/7916117/working/building/REAL250005036372 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036372 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036372/0 /scratch/stefan/7916117/working/building/REAL250005036372 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/966 `/scratch/stefan/7916117/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=CN1C) `REAL250005036372.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036372 none CC1=CC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 195, 195, 114, 114, 114, 22, 8, 1, 1, 1, 1, 1, 1, 1, 195, 195, 195, 195, 195, 195, 195, 113, 22, 22, 8, 8, 195, 195, 195, 195] 195 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036372 none CC1=CC(=O)C(C(=O)NCCC2=NC(=O)O[N-]2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 72, 107, 195, 195, 195, 195, 195, 1, 1, 1, 1, 1, 1, 1, 13, 72, 72, 107, 107, 1, 2, 2, 2] 195 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 29] set([32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036372 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036372 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036372/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036372 Building REAL250005036373 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036373' /scratch/stefan/7916117/working/building/REAL250005036373 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036373 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036373/0 /scratch/stefan/7916117/working/building/REAL250005036373 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/967 `/scratch/stefan/7916117/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CO1) `REAL250005036373.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036373 none COC(=O)CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 148, 201, 83, 83, 36, 36, 36, 8, 8, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 201, 201, 201, 148, 148, 35, 8, 8, 8, 8, 83, 83] 201 rigid atoms, others: [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]) 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: REAL250005036373 none COC(=O)CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [34, 33, 7, 34, 1, 1, 1, 1, 6, 6, 6, 24, 24, 83, 83, 83, 83, 83, 1, 1, 1, 34, 34, 34, 7, 7, 6, 24, 24, 24, 24, 1, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 18, 19, 20, 31] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036373 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036373 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036373/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036373 Building REAL250005036374 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036374' /scratch/stefan/7916117/working/building/REAL250005036374 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036374 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036374/0 /scratch/stefan/7916117/working/building/REAL250005036374 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/968 `/scratch/stefan/7916117/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC2=CNN=C2C(C(=O)NCCC2=NC(=O)O[N-]2)C1) `REAL250005036374.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036374 none CC1CC2=CNN=C2C(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 25, 24, 8, 8, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 608 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036374 none CC1CC2=CNN=C2C(C(=O)NCCC2=NC(=O)O[N-]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 68, 103, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 12, 68, 68, 103, 103, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 20, 24, 25, 26, 27, 28, 29, 36] set([32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 30, 31]) total number of confs: 602 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036374 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036374 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036374/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036374 Building REAL250005036375 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036375' /scratch/stefan/7916117/working/building/REAL250005036375 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036375 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036375/0 /scratch/stefan/7916117/working/building/REAL250005036375 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/969 `/scratch/stefan/7916117/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1(C(=O)NCCC2=NC(=O)O[N-]2)CC1) `REAL250005036375.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036375 none C[NH+](C)CC1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 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, 15, 15, 15, 8, 5, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 8, 8, 5, 5, 18, 18, 18, 18] 18 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL250005036375 none C[NH+](C)CC1(C(=O)NCCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 9, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 4, 4, 4, 9, 9, 18, 18, 18, 18, 18, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 4, 9, 9, 9, 9, 1, 1, 1, 1] 18 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 17, 18] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036375 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036375 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036375/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036375 Building REAL250005036376 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036376' /scratch/stefan/7916117/working/building/REAL250005036376 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036376 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036376/0 /scratch/stefan/7916117/working/building/REAL250005036376 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/970 `/scratch/stefan/7916117/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C(C1CCC1)C1CCC1) `REAL250005036376.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036376 none O=C(NCCC1=NC(=O)O[N-]1)C(C1CCC1)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 4, 14, 14, 40, 40, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 4, 6, 6, 6, 14, 40, 40, 40, 40, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 71 rigid atoms, others: [32, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 201 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: REAL250005036376 none O=C(NCCC1=NC(=O)O[N-]1)C(C1CCC1)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 35, 8, 8, 1, 1, 1, 1, 1, 1, 1, 34, 70, 71, 71, 71, 69, 71, 71, 71, 34, 8, 8, 8, 8, 70, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71, 71] 71 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 275 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: REAL250005036376 none O=C(NCCC1=NC(=O)O[N-]1)C(C1CCC1)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 4, 14, 14, 40, 40, 71, 71, 71, 71, 71, 1, 4, 6, 6, 6, 1, 1, 1, 1, 14, 40, 40, 40, 40, 4, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1] 71 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 11, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 201 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036376 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036376 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036376/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036376 Building REAL250005036377 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036377' /scratch/stefan/7916117/working/building/REAL250005036377 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036377 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036377/0 /scratch/stefan/7916117/working/building/REAL250005036377 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/971 `/scratch/stefan/7916117/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036377.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036377 none CC1=NC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 135, 40, 40, 40, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 135, 135, 40, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036377 none CC1=NC=CC=C1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 30, 30, 30, 102, 104, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 6, 6, 30, 102, 102, 104, 104] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 557 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036377 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036377 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036377/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036377 Building REAL250005036378 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036378' /scratch/stefan/7916117/working/building/REAL250005036378 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036378 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036378/0 /scratch/stefan/7916117/working/building/REAL250005036378 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/972 `/scratch/stefan/7916117/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC=C1) `REAL250005036378.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036378 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 54, 61, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 11, 54, 54, 61, 61, 1, 1, 4, 4, 1, 4, 4] 201 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 319 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036378 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 19, 9, 1, 1, 1, 1, 1, 1, 1, 52, 112, 114, 114, 114, 114, 201, 201, 114, 201, 201, 52, 19, 19, 9, 9, 114, 114, 201, 201, 114, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 713 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: REAL250005036378 none O=C(NCCC1=NC(=O)O[N-]1)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 30, 30, 111, 117, 201, 201, 201, 201, 201, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 30, 111, 111, 117, 117, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 14, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 576 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036378 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036378 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036378/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036378 Building REAL250005036379 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036379' /scratch/stefan/7916117/working/building/REAL250005036379 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036379 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036379/0 /scratch/stefan/7916117/working/building/REAL250005036379 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/973 `/scratch/stefan/7916117/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC([NH2+]C(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036379.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036379 none CCC([NH2+]C(C)C)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 6, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [67, 47, 35, 47, 62, 62, 62, 67, 67, 35, 35, 16, 8, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 47, 67, 67, 67, 67, 67, 67, 67, 35, 16, 16, 8, 8] 81 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 428 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036379 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036379 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036379/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036379 Building REAL250005036380 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036380' /scratch/stefan/7916117/working/building/REAL250005036380 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036380 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036380/0 /scratch/stefan/7916117/working/building/REAL250005036380 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/974 `/scratch/stefan/7916117/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)C=CS1) `REAL250005036380.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036380 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [7, 1, 7, 7, 39, 71, 184, 184, 184, 184, 184, 1, 1, 1, 1, 1, 1, 7, 39, 39, 71, 71, 1, 1] 184 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21]) total number of confs: 481 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036380 none O=C(NCCC1=NC(=O)O[N-]1)C1=C(Cl)C=CS1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [78, 78, 24, 8, 1, 1, 1, 1, 1, 1, 1, 78, 184, 184, 184, 184, 184, 78, 25, 25, 8, 8, 184, 184] 184 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036380 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036380 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036380/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036380 Building REAL250005036381 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036381' /scratch/stefan/7916117/working/building/REAL250005036381 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036381 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036381/0 /scratch/stefan/7916117/working/building/REAL250005036381 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/975 `/scratch/stefan/7916117/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=COC2=CC=CC=C12)NCCC1=NC(=O)O[N-]1) `REAL250005036381.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036381 none O=C(CC1=COC2=CC=CC=C12)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [34, 34, 34, 105, 201, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 201, 201, 201, 201, 201, 34, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 547 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036381 none O=C(CC1=COC2=CC=CC=C12)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 108, 110, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 35, 108, 108, 110, 110] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27] set([0, 1, 32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31]) total number of confs: 580 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036381 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036381 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036381/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036381 Building REAL250005036382 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036382' /scratch/stefan/7916117/working/building/REAL250005036382 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036382 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036382/0 /scratch/stefan/7916117/working/building/REAL250005036382 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/976 `/scratch/stefan/7916117/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC=C1COCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036382.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036382 none CN1N=CC=C1COCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 156, 102, 86, 31, 31, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 156, 156, 86, 86, 31, 7, 7, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 723 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036382 none CN1N=CC=C1COCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 7, 25, 53, 67, 67, 67, 120, 120, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 7, 7, 53, 53, 67, 120, 120, 120, 120] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 650 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036382 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036382 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036382/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036382 Building REAL250005036383 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036383' /scratch/stefan/7916117/working/building/REAL250005036383 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036383 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036383/0 /scratch/stefan/7916117/working/building/REAL250005036383 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/977 `/scratch/stefan/7916117/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC1=CC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036383.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036383 none CNC1=CC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 197, 174, 201, 201, 75, 76, 76, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 75, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 573 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: REAL250005036383 none CNC1=CC=CC=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 57, 88, 201, 201, 201, 201, 201, 6, 6, 6, 6, 1, 1, 1, 1, 12, 57, 57, 88, 88] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 554 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036383 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036383 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036383/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036383 Building REAL250005036384 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036384' /scratch/stefan/7916117/working/building/REAL250005036384 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036384 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036384/0 /scratch/stefan/7916117/working/building/REAL250005036384 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/978 `/scratch/stefan/7916117/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)NC2=N1) `REAL250005036384.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036384 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)NC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 11, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 63, 81, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 63, 63, 81, 81, 1, 1, 1, 1] 127 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 401 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036384 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C2NC(=O)NC2=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 11, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 3, 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: [82, 82, 23, 8, 1, 1, 1, 1, 1, 1, 1, 82, 127, 127, 127, 127, 127, 127, 127, 127, 127, 82, 23, 23, 8, 8, 127, 127, 127, 127] 127 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036384 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036384 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036384/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036384 Building REAL250005036385 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036385' /scratch/stefan/7916117/working/building/REAL250005036385 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036385 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036385/0 /scratch/stefan/7916117/working/building/REAL250005036385 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/979 `/scratch/stefan/7916117/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1) `REAL250005036385.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036385 none COCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 151, 65, 65, 65, 19, 8, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 201, 201, 201, 201, 201, 65, 19, 19, 8, 8, 151, 151, 151, 151, 151, 151] 201 rigid atoms, others: [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, 33]) 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: REAL250005036385 none COCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [18, 9, 1, 1, 1, 7, 7, 7, 38, 49, 151, 151, 151, 151, 151, 1, 1, 1, 18, 18, 18, 9, 9, 7, 38, 38, 49, 49, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036385 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036385 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036385/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036385 Building REAL250005036386 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036386' /scratch/stefan/7916117/working/building/REAL250005036386 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036386 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036386/0 /scratch/stefan/7916117/working/building/REAL250005036386 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/980 `/scratch/stefan/7916117/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=[NH+]C=C2C=C1) `REAL250005036386.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036386 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=[NH+]C=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 6, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 39, 53, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 53, 53, 1, 1, 1, 1, 1] 95 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) 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: REAL250005036386 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=[NH+]C=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 6, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 17, 8, 1, 1, 1, 1, 1, 1, 1, 63, 95, 95, 95, 95, 95, 95, 95, 95, 95, 63, 17, 17, 8, 8, 95, 95, 95, 95, 95] 95 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036386 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036386/1 /scratch/stefan/7916117/working/building/REAL250005036386 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/981 `/scratch/stefan/7916117/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=NC=C2C=C1) `REAL250005036386.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036386 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=NC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 49, 79, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 49, 49, 79, 79, 1, 1, 1, 1, 1] 147 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 446 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036386 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN2C=NC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 22, 8, 1, 1, 1, 1, 1, 1, 1, 61, 147, 147, 147, 147, 147, 147, 147, 147, 61, 22, 22, 8, 8, 147, 147, 147, 147, 147] 147 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036386 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036386 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036386/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036386/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036386 Building REAL250005036387 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036387' /scratch/stefan/7916117/working/building/REAL250005036387 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036387 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036387/0 /scratch/stefan/7916117/working/building/REAL250005036387 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/982 `/scratch/stefan/7916117/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1O) `REAL250005036387.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036387 none CC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 146, 201, 146, 146, 146, 54, 54, 54, 19, 8, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 201, 201, 201, 146, 146, 54, 19, 19, 8, 8, 146, 292] 402 rigid atoms, others: [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]) total number of confs: 804 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036387 none CC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 9, 1, 1, 1, 1, 1, 5, 5, 5, 29, 46, 146, 146, 146, 146, 146, 1, 1, 1, 9, 9, 9, 1, 1, 5, 29, 29, 46, 46, 1, 2] 402 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 19, 20, 24, 25, 31] set([0, 32, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036387 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036387 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036387/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036387 Building REAL250005036388 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036388' /scratch/stefan/7916117/working/building/REAL250005036388 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036388 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036388/0 /scratch/stefan/7916117/working/building/REAL250005036388 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/983 `/scratch/stefan/7916117/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CC=CN=C21) `REAL250005036388.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036388 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [12, 1, 12, 12, 74, 113, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 74, 74, 113, 113, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 613 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: REAL250005036388 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=CC=CN=C21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 1, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 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: [100, 100, 24, 8, 1, 1, 1, 1, 1, 1, 1, 99, 201, 201, 201, 201, 201, 201, 201, 201, 99, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 599 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036388 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036388 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036388/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036388 Building REAL250005036389 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036389' /scratch/stefan/7916117/working/building/REAL250005036389 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036389 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036389/0 /scratch/stefan/7916117/working/building/REAL250005036389 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/984 `/scratch/stefan/7916117/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(NC(N)=O)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036389.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036389 none CC(C)(C)C(NC(N)=O)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [109, 107, 109, 107, 73, 109, 114, 114, 114, 73, 73, 22, 8, 1, 1, 1, 1, 1, 1, 1, 109, 109, 109, 109, 109, 109, 109, 109, 109, 109, 114, 114, 114, 72, 23, 23, 8, 8] 114 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 475 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036389 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036389 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036389/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036389 Building REAL250005036390 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036390' /scratch/stefan/7916117/working/building/REAL250005036390 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036390 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036390/0 /scratch/stefan/7916117/working/building/REAL250005036390 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/985 `/scratch/stefan/7916117/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C)=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036390.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036390 none CC1=COC(C)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 100, 100, 100, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 99, 24, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 454 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: REAL250005036390 none CC1=COC(C)=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 56, 82, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 11, 56, 56, 82, 82] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 524 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036390 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036390 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036390/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036390 Building REAL250005036391 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036391' /scratch/stefan/7916117/working/building/REAL250005036391 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036391 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036391/0 /scratch/stefan/7916117/working/building/REAL250005036391 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/986 `/scratch/stefan/7916117/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOCC1) `REAL250005036391.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036391 none COC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 186, 98, 98, 98, 24, 8, 1, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 201, 201, 201, 98, 24, 24, 8, 8, 186, 186, 186, 186, 186, 186, 186, 186] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 607 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036391 none COC1(C(=O)NCCC2=NC(=O)O[N-]2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [10, 1, 1, 1, 5, 5, 5, 31, 52, 186, 186, 186, 186, 186, 1, 1, 1, 1, 1, 10, 10, 10, 5, 31, 31, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 33, 34, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 397 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036391 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036391 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036391/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036391 Building REAL250005036392 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036392' /scratch/stefan/7916117/working/building/REAL250005036392 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036392 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036392/0 /scratch/stefan/7916117/working/building/REAL250005036392 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/987 `/scratch/stefan/7916117/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=N1) `REAL250005036392.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036392 none COCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 179, 119, 119, 59, 59, 59, 19, 8, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 201, 201, 201, 179, 179, 59, 19, 19, 8, 8, 119] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL250005036392 none COCC1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 1, 9, 9, 9, 30, 36, 119, 119, 119, 119, 119, 1, 1, 1, 16, 16, 16, 7, 7, 9, 30, 30, 36, 36, 1] 201 rigid atoms, others: [2, 3, 4, 5, 16, 17, 18, 29] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036392 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036392 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036392/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036392 Building REAL250005036393 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036393' /scratch/stefan/7916117/working/building/REAL250005036393 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036393 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036393/0 /scratch/stefan/7916117/working/building/REAL250005036393 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/988 `/scratch/stefan/7916117/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC=C1) `REAL250005036393.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036393 none CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 103, 103, 103, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 24, 24, 8, 8, 201, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 453 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: REAL250005036393 none CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 11, 11, 11, 55, 89, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 11, 55, 55, 89, 89, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 16, 17, 18, 31] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 563 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036393 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036393 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036393/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036393 Building REAL250005036394 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036394' /scratch/stefan/7916117/working/building/REAL250005036394 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036394 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036394/0 /scratch/stefan/7916117/working/building/REAL250005036394 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/989 `/scratch/stefan/7916117/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CC(=O)NCCC2=NC(=O)O[N-]2)CC1(Cl)Cl) `REAL250005036394.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036394 none CC1(CC(=O)NCCC2=NC(=O)O[N-]2)CC1(Cl)Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'Cl', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 16, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 175, 62, 62, 62, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 175, 175, 62, 19, 19, 8, 8, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036394 none CC1(CC(=O)NCCC2=NC(=O)O[N-]2)CC1(Cl)Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'Cl', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 16, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 7, 26, 26, 26, 103, 108, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 7, 7, 26, 103, 103, 108, 108, 1, 1] 201 rigid atoms, others: [0, 1, 2, 14, 15, 16, 17, 28, 29] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036394 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036394 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036394/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036394 Building REAL250005036395 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036395' /scratch/stefan/7916117/working/building/REAL250005036395 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036395 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036395/0 /scratch/stefan/7916117/working/building/REAL250005036395 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/990 `/scratch/stefan/7916117/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NN(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036395.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036395 none COCC1=NN(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 181, 116, 116, 116, 116, 116, 116, 53, 53, 53, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 181, 181, 116, 116, 116, 116, 53, 17, 17, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 652 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036395 none COCC1=NN(C)C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 27, 116, 116, 116, 116, 116, 24, 24, 24, 7, 7, 2, 2, 2, 1, 5, 23, 23, 27, 27] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036395 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036395 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036395/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036395 Building REAL250005036396 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036396' /scratch/stefan/7916117/working/building/REAL250005036396 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036396 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036396/0 /scratch/stefan/7916117/working/building/REAL250005036396 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/991 `/scratch/stefan/7916117/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl) `REAL250005036396.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036396 none CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 74, 74, 74, 24, 8, 1, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 74, 24, 24, 8, 8, 131] 131 rigid atoms, others: [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]) total number of confs: 331 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036396 none CN1N=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 56, 83, 131, 131, 131, 131, 131, 1, 1, 1, 2, 2, 2, 12, 55, 55, 83, 83, 1] 131 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036396 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036396 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036396/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036396 Building REAL250005036397 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036397' /scratch/stefan/7916117/working/building/REAL250005036397 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036397 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036397/0 /scratch/stefan/7916117/working/building/REAL250005036397 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/992 `/scratch/stefan/7916117/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=NC=C2S1) `REAL250005036397.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036397 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 63, 90, 148, 148, 148, 149, 149, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 62, 62, 90, 90, 1, 1, 1, 1] 149 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 471 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036397 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=NC=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 22, 8, 1, 1, 1, 1, 1, 1, 1, 77, 149, 149, 149, 149, 148, 148, 148, 148, 77, 22, 22, 8, 8, 149, 149, 149, 149] 149 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036397 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036397 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036397/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036397 Building REAL250005036398 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036398' /scratch/stefan/7916117/working/building/REAL250005036398 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036398 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036398/0 /scratch/stefan/7916117/working/building/REAL250005036398 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/993 `/scratch/stefan/7916117/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NC=C1C(N)=O) `REAL250005036398.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036398 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 8, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 86, 86, 86, 24, 8, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 201, 201, 138, 138, 138, 138, 86, 24, 25, 8, 8, 138, 201, 201] 201 rigid atoms, others: [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]) total number of confs: 604 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036398 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NC=C1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 8, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 37, 47, 138, 138, 138, 138, 138, 1, 1, 1, 1, 4, 4, 2, 2, 2, 1, 10, 37, 37, 47, 47, 1, 4, 4] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 18, 24, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 31, 32]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036398 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036398 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036398/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036398 Building REAL250005036399 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036399' /scratch/stefan/7916117/working/building/REAL250005036399 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036399 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036399/0 /scratch/stefan/7916117/working/building/REAL250005036399 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/994 `/scratch/stefan/7916117/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2O1) `REAL250005036399.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036399 none CC1CC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 180, 180, 180, 180, 80, 80, 80, 24, 8, 1, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 180, 180, 180, 180, 180, 180, 180, 80, 24, 24, 8, 8] 180 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL250005036399 none CC1CC2=CC=CC(C(=O)NCCC3=NC(=O)O[N-]3)=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 12, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 67, 88, 180, 180, 180, 180, 180, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 13, 67, 67, 88, 88] 180 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 24, 25, 26, 27, 28, 29] set([32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31]) total number of confs: 498 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036399 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036399 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036399/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036399 Building REAL250005036400 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036400' /scratch/stefan/7916117/working/building/REAL250005036400 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036400 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036400/0 /scratch/stefan/7916117/working/building/REAL250005036400 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/995 `/scratch/stefan/7916117/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CC2CC2)N=N1) `REAL250005036400.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036400 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CC2CC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 31, 81, 81, 81, 81, 81, 1, 1, 1, 1, 9, 25, 25, 1, 1, 7, 27, 27, 31, 31, 1, 9, 9, 25, 25, 25, 25, 25] 201 rigid atoms, others: [1, 11, 12, 13, 14, 18, 19, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16, 17, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036400 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CC2CC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 51, 20, 8, 1, 1, 1, 1, 1, 1, 1, 51, 81, 81, 81, 143, 201, 201, 81, 81, 50, 20, 20, 8, 8, 81, 143, 143, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 803 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036400 none O=C(NCCC1=NC(=O)O[N-]1)C1=CN(CC2CC2)N=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 56, 56, 113, 121, 201, 201, 201, 201, 201, 25, 25, 6, 1, 1, 1, 1, 25, 25, 56, 113, 113, 121, 121, 25, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036400 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036400 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036400/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036400 Building REAL250005036401 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036401' /scratch/stefan/7916117/working/building/REAL250005036401 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036401 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036401/0 /scratch/stefan/7916117/working/building/REAL250005036401 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/996 `/scratch/stefan/7916117/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CN=C2S1) `REAL250005036401.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036401 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 63, 91, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 63, 63, 91, 91, 1, 1, 1, 1] 145 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 471 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036401 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=CN=C2S1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [75, 75, 24, 8, 1, 1, 1, 1, 1, 1, 1, 75, 145, 145, 145, 145, 144, 145, 145, 145, 74, 24, 24, 8, 8, 145, 145, 145, 145] 145 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 355 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036401 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036401 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036401/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036401 Building REAL250005036402 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036402' /scratch/stefan/7916117/working/building/REAL250005036402 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036402 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036402/0 /scratch/stefan/7916117/working/building/REAL250005036402 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/997 `/scratch/stefan/7916117/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=NC=C2C=C1) `REAL250005036402.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036402 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=NC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 39, 64, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 64, 64, 1, 1, 1, 1, 1, 1] 117 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036402 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=CC=NC=C2C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 21, 8, 1, 1, 1, 1, 1, 1, 1, 52, 117, 117, 117, 117, 117, 117, 117, 117, 117, 51, 21, 21, 8, 8, 117, 117, 117, 117, 117, 117] 117 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036402 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036402 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036402/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036402 Building REAL250005036403 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036403' /scratch/stefan/7916117/working/building/REAL250005036403 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036403 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036403/0 /scratch/stefan/7916117/working/building/REAL250005036403 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/998 `/scratch/stefan/7916117/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C2=C1CCC2) `REAL250005036403.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036403 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 183, 198, 198, 92, 92, 92, 23, 8, 1, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 198, 198, 198, 198, 198, 198, 91, 23, 23, 8, 8, 198, 198, 198, 198, 198, 198] 198 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 497 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036403 none CC1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C2=C1CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 11, 61, 89, 198, 198, 198, 198, 198, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 11, 61, 61, 89, 89, 1, 1, 1, 1, 1, 1] 198 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 32, 34, 16, 17, 18, 19, 20, 24, 25, 33, 36, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 540 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036403 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036403 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036403/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036403 Building REAL250005036404 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036404' /scratch/stefan/7916117/working/building/REAL250005036404 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036404 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036404/0 /scratch/stefan/7916117/working/building/REAL250005036404 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/999 `/scratch/stefan/7916117/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CS1) `REAL250005036404.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036404 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 109, 109, 109, 24, 8, 1, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 197, 109, 24, 24, 8, 8, 197, 197] 197 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 457 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036404 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 59, 99, 197, 197, 197, 197, 197, 1, 1, 1, 2, 2, 2, 9, 59, 59, 99, 99, 1, 1] 197 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036404 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036404 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036404/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036404 Building REAL250005036405 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036405' /scratch/stefan/7916117/working/building/REAL250005036405 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005036405 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036405/0 /scratch/stefan/7916117/working/building/REAL250005036405 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1000 `/scratch/stefan/7916117/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NNN=C1)NCCC1=NC(=O)O[N-]1) `REAL250005036405.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036405 none O=C(CCC1=NNN=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 8, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [47, 47, 47, 143, 178, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 143, 143, 178, 178, 201, 201, 47, 17, 17, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036405 none O=C(CCC1=NNN=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 8, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [50, 14, 8, 1, 1, 1, 1, 1, 1, 50, 50, 125, 128, 201, 201, 201, 201, 201, 14, 14, 8, 8, 1, 1, 50, 129, 129, 128, 128] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 642 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036405 /scratch/stefan/7916117/working /scratch/stefan/7916117 mkdir: created directory `1' /scratch/stefan/7916117/working/building/REAL250005036405/1 /scratch/stefan/7916117/working/building/REAL250005036405 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 1 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1001 `/scratch/stefan/7916117/working/3D/1001' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CNN=N1)NCCC1=NC(=O)O[N-]1) `REAL250005036405.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005036405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036405 none O=C(CCC1=CNN=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [56, 56, 56, 156, 168, 201, 201, 201, 201, 23, 8, 1, 1, 1, 1, 1, 1, 1, 156, 156, 168, 168, 201, 201, 56, 23, 23, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 722 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036405 none O=C(CCC1=CNN=N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [46, 14, 8, 1, 1, 1, 1, 1, 1, 46, 46, 111, 124, 201, 201, 201, 201, 201, 14, 14, 8, 8, 1, 1, 46, 114, 114, 123, 123] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 22, 23] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28]) total number of confs: 630 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036405 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036405 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036405/0.* 1: /scratch/stefan/7916117/working/building/REAL250005036405/1.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036405 Building REAL250005036406 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036406' /scratch/stefan/7916117/working/building/REAL250005036406 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036406 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036406/0 /scratch/stefan/7916117/working/building/REAL250005036406 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1002 `/scratch/stefan/7916117/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C(C)C) `REAL250005036406.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036406 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 5, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 100, 100, 100, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 24, 24, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [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, 33, 34, 35]) total number of confs: 446 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: REAL250005036406 none CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=NN1C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 5, 5, 5, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 66, 93, 201, 201, 201, 201, 201, 1, 1, 1, 5, 5, 2, 2, 2, 1, 13, 66, 66, 93, 93, 5, 5, 6, 6, 6, 6, 6] 201 rigid atoms, others: [0, 1, 2, 3, 4, 15, 16, 17, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 571 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036406 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036406 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036406/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036406 Building REAL250005036407 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036407' /scratch/stefan/7916117/working/building/REAL250005036407 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036407 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036407/0 /scratch/stefan/7916117/working/building/REAL250005036407 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1003 `/scratch/stefan/7916117/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=N1) `REAL250005036407.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036407 none CN1N=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 145, 119, 39, 39, 39, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 145, 145, 119, 119, 39, 15, 15, 7, 7] 201 rigid atoms, others: [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]) 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: REAL250005036407 none CN1N=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 8, 13, 52, 52, 52, 124, 124, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 8, 8, 13, 13, 52, 126, 126, 126, 126] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036407 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036407 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036407/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036407 Building REAL250005036408 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036408' /scratch/stefan/7916117/working/building/REAL250005036408 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036408 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036408/0 /scratch/stefan/7916117/working/building/REAL250005036408 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1004 `/scratch/stefan/7916117/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(F)(F)F)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036408.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036408 none CCC(CC(F)(F)F)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 15, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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: [160, 139, 69, 139, 196, 196, 196, 196, 69, 69, 19, 8, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 172, 139, 196, 196, 69, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 1124 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036408 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036408 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036408/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036408 Building REAL250005036409 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036409' /scratch/stefan/7916117/working/building/REAL250005036409 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036409 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036409/0 /scratch/stefan/7916117/working/building/REAL250005036409 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1005 `/scratch/stefan/7916117/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC2CC21)NCCC1=NC(=O)O[N-]1) `REAL250005036409.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036409 none O=C(CC1CCC2CC21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [54, 54, 54, 184, 201, 201, 201, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 184, 184, 201, 201, 201, 201, 201, 201, 201, 201, 201, 54, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 763 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036409 none O=C(CC1CCC2CC21)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [33, 7, 1, 1, 1, 1, 1, 1, 1, 33, 33, 113, 116, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 113, 113, 116, 116] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 33, 32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036409 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036409 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036409/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036409 Building REAL250005036410 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036410' /scratch/stefan/7916117/working/building/REAL250005036410 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036410 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036410/0 /scratch/stefan/7916117/working/building/REAL250005036410 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1006 `/scratch/stefan/7916117/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(F)C(CC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036410.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036410 none CC1=CC=C(F)C(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 109, 25, 25, 25, 13, 8, 1, 1, 1, 1, 1, 1, 1, 170, 201, 201, 201, 201, 201, 109, 109, 25, 13, 13, 8, 8, 201] 201 rigid atoms, others: [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]) total number of confs: 631 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036410 none CC1=CC=C(F)C(CC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 7, 35, 35, 35, 121, 121, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 7, 7, 35, 121, 121, 121, 121, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 19, 32, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036410 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036410 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036410/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036410 Building REAL250005036411 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036411' /scratch/stefan/7916117/working/building/REAL250005036411 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036411 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036411/0 /scratch/stefan/7916117/working/building/REAL250005036411 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1007 `/scratch/stefan/7916117/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1) `REAL250005036411.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036411 none C=CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 123, 67, 67, 67, 19, 8, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 201, 201, 201, 201, 201, 67, 19, 19, 8, 8, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123] 201 rigid atoms, others: [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, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 857 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036411 none C=CCC1(C(=O)NCCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 1, 1, 2, 2, 2, 14, 22, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 15, 15, 15, 7, 7, 2, 14, 14, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 37, 35, 39, 34, 15, 16, 17, 18, 19, 36, 38, 30, 31] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036411 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036411 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036411/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036411 Building REAL250005036412 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036412' /scratch/stefan/7916117/working/building/REAL250005036412 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036412 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036412/0 /scratch/stefan/7916117/working/building/REAL250005036412 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1008 `/scratch/stefan/7916117/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036412.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036412 none CC1=CN=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 129, 125, 45, 45, 45, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 129, 129, 125, 125, 45, 17, 17, 8, 8, 201] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 676 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036412 none CC1=CN=CC(CCC(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 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, 6, 4, 7, 7, 7, 7, 7, 5, 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, 1, 1, 2, 6, 24, 24, 25, 114, 116, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 2, 2, 6, 6, 25, 114, 114, 116, 116, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 19, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 581 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036412 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036412 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036412/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036412 Building REAL250005036413 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036413' /scratch/stefan/7916117/working/building/REAL250005036413 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036413 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036413/0 /scratch/stefan/7916117/working/building/REAL250005036413 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1009 `/scratch/stefan/7916117/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CN=CN=C1)NCCC1=NC(=O)O[N-]1) `REAL250005036413.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036413 none O=C(CCC1=CN=CN=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 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: [66, 66, 66, 169, 183, 201, 201, 191, 201, 201, 19, 8, 1, 1, 1, 1, 1, 1, 1, 168, 168, 183, 183, 201, 201, 201, 65, 19, 19, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 835 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036413 none O=C(CCC1=CN=CN=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 5, 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: [35, 8, 5, 1, 1, 1, 1, 1, 1, 1, 35, 35, 98, 109, 201, 201, 201, 201, 201, 8, 8, 5, 5, 1, 1, 1, 35, 99, 99, 109, 108] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24, 25] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30]) total number of confs: 583 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036413 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036413 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036413/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036413 Building REAL250005036414 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036414' /scratch/stefan/7916117/working/building/REAL250005036414 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036414 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036414/0 /scratch/stefan/7916117/working/building/REAL250005036414 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1010 `/scratch/stefan/7916117/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(C(C)C)=N1) `REAL250005036414.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036414 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 65, 65, 65, 21, 8, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 201, 201, 155, 155, 155, 155, 65, 21, 21, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: REAL250005036414 none CC1=C(C(=O)NCCC2=NC(=O)O[N-]2)OC(C(C)C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 12, 1, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 35, 49, 155, 155, 155, 155, 155, 1, 1, 1, 12, 12, 1, 2, 2, 2, 7, 35, 35, 49, 49, 12, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 14, 15, 16, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036414 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036414 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036414/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036414 Building REAL250005036415 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036415' /scratch/stefan/7916117/working/building/REAL250005036415 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036415 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036415/0 /scratch/stefan/7916117/working/building/REAL250005036415 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1011 `/scratch/stefan/7916117/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1) `REAL250005036415.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036415 none CC(F)(F)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 148, 197, 197, 92, 188, 188, 92, 92, 92, 24, 8, 1, 1, 1, 1, 1, 1, 1, 188, 188, 197, 197, 197, 188, 188, 92, 24, 24, 8, 8, 188, 188] 197 rigid atoms, others: [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]) total number of confs: 1027 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036415 none CC(F)(F)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 37, 71, 188, 188, 188, 188, 188, 1, 1, 7, 7, 7, 1, 1, 7, 37, 37, 71, 71, 1, 1] 197 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 19, 20, 24, 25, 31] set([0, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 484 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036415 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036415 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036415/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036415 Building REAL250005036416 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036416' /scratch/stefan/7916117/working/building/REAL250005036416 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036416 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036416/0 /scratch/stefan/7916117/working/building/REAL250005036416 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1012 `/scratch/stefan/7916117/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(CC(C)C)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036416.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036416 none CC(C)CC(CC(C)C)C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 74, 48, 72, 75, 75, 75, 47, 48, 8, 8, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 81, 81, 74, 75, 75, 75, 75, 75, 75, 75, 75, 75, 47, 8, 8, 8, 8] 81 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 304 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036416 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036416 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036416/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036416 Building REAL250005036417 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036417' /scratch/stefan/7916117/working/building/REAL250005036417 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036417 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036417/0 /scratch/stefan/7916117/working/building/REAL250005036417 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1013 `/scratch/stefan/7916117/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC(=O)C1CC1)NCCC1=NC(=O)O[N-]1) `REAL250005036417.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036417 none O=C(CCCC(=O)C1CC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [50, 50, 50, 79, 56, 87, 150, 150, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 81, 81, 201, 201, 201, 201, 201, 50, 17, 17, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 899 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036417 none O=C(CCCC(=O)C1CC1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 5, 5, 5, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 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: [70, 57, 52, 49, 9, 1, 9, 1, 1, 1, 69, 70, 129, 129, 201, 201, 201, 201, 201, 57, 57, 52, 52, 49, 49, 1, 1, 1, 1, 1, 70, 129, 129, 129, 129] 201 rigid atoms, others: [5, 7, 8, 9, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036417 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036417 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036417/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036417 Building REAL250005036418 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036418' /scratch/stefan/7916117/working/building/REAL250005036418 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036418 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036418/0 /scratch/stefan/7916117/working/building/REAL250005036418 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1014 `/scratch/stefan/7916117/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1CCC1) `REAL250005036418.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036418 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 72, 78, 201, 201, 201, 201, 201, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 17, 72, 72, 78, 78, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 476 number of broken/clashed sets: 153 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036418 none CC(C)(C(=O)NCCC1=NC(=O)O[N-]1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 133, 33, 33, 17, 8, 1, 1, 1, 1, 1, 1, 1, 133, 201, 201, 201, 133, 133, 133, 133, 133, 133, 33, 17, 17, 8, 8, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 772 number of broken/clashed sets: 153 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036418 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036418 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036418/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036418 Building REAL250005036419 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036419' /scratch/stefan/7916117/working/building/REAL250005036419 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036419 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036419/0 /scratch/stefan/7916117/working/building/REAL250005036419 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1015 `/scratch/stefan/7916117/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCC2=NC(=O)O[N-]2)CC=CCC1) `REAL250005036419.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036419 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 65, 65, 65, 21, 8, 1, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 166, 166, 166, 166, 65, 21, 21, 8, 8, 166, 166, 166, 166, 166, 166, 166, 166] 166 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 502 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036419 none CC1(C(=O)NCCC2=NC(=O)O[N-]2)CC=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 7, 7, 7, 46, 84, 166, 166, 166, 166, 166, 1, 1, 1, 1, 1, 2, 2, 2, 7, 46, 46, 84, 84, 1, 1, 1, 1, 1, 1, 1, 1] 166 rigid atoms, others: [0, 1, 2, 33, 32, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036419 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036419 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036419/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036419 Building REAL250005036420 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036420' /scratch/stefan/7916117/working/building/REAL250005036420 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036420 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036420/0 /scratch/stefan/7916117/working/building/REAL250005036420 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1016 `/scratch/stefan/7916117/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCSCC2) `REAL250005036420.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036420 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCSCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 1, 8, 8, 28, 41, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 1, 1, 8, 28, 28, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 112 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005036420 none O=C(NCCC1=NC(=O)O[N-]1)C1CC12CCSCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [71, 71, 23, 8, 1, 1, 1, 1, 1, 1, 1, 71, 112, 112, 112, 112, 112, 112, 112, 71, 23, 23, 8, 8, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112] 112 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036420 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036420 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036420/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036420 Building REAL250005036421 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036421' /scratch/stefan/7916117/working/building/REAL250005036421 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036421 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036421/0 /scratch/stefan/7916117/working/building/REAL250005036421 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1017 `/scratch/stefan/7916117/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=N1) `REAL250005036421.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036421 none CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 93, 93, 93, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 21, 21, 8, 8, 201] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036421 none CC(C)C1=C(C(=O)NCCC2=NC(=O)O[N-]2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 10, 10, 10, 54, 86, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 54, 54, 86, 86, 1] 201 rigid atoms, others: [1, 3, 4, 5, 16, 17, 18, 31] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036421 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036421 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036421/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036421 Building REAL250005036422 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036422' /scratch/stefan/7916117/working/building/REAL250005036422 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036422 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036422/0 /scratch/stefan/7916117/working/building/REAL250005036422 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1018 `/scratch/stefan/7916117/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=CC=NN2C=C1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036422.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036422 none CC1=NC2=CC=NN2C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 173, 173, 173, 173, 173, 173, 90, 90, 90, 24, 8, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 173, 173, 90, 24, 24, 8, 8] 173 rigid atoms, others: [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]) total number of confs: 405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036422 none CC1=NC2=CC=NN2C=C1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 1, 1, 1, 1, 1, 10, 10, 10, 63, 97, 173, 173, 173, 173, 173, 2, 2, 2, 1, 1, 1, 10, 63, 63, 97, 97] 173 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31]) total number of confs: 533 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036422 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036422 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036422/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036422 Building REAL250005036423 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036423' /scratch/stefan/7916117/working/building/REAL250005036423 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036423 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036423/0 /scratch/stefan/7916117/working/building/REAL250005036423 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1019 `/scratch/stefan/7916117/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CSC(F)F)NCCC1=NC(=O)O[N-]1) `REAL250005036423.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036423 none O=C(CSC(F)F)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 14, 5, 15, 15, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 112, 177, 201, 201, 17, 7, 1, 1, 1, 1, 1, 1, 1, 112, 112, 201, 43, 17, 17, 7, 7] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 715 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036423 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036423 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036423/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036423 Building REAL250005036424 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036424' /scratch/stefan/7916117/working/building/REAL250005036424 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036424 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036424/0 /scratch/stefan/7916117/working/building/REAL250005036424 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1020 `/scratch/stefan/7916117/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)C2CC2)CC1) `REAL250005036424.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036424 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 15, 18, 91, 91, 91, 91, 91, 1, 1, 4, 4, 19, 19, 1, 1, 3, 15, 15, 18, 18, 19, 19, 19, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 11, 12, 17, 18, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036424 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 17, 8, 1, 1, 1, 1, 1, 1, 1, 57, 91, 152, 152, 201, 201, 91, 91, 57, 17, 17, 8, 8, 201, 201, 201, 201, 201, 91, 91, 91, 91] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 746 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036424 none O=C(NCCC1=NC(=O)O[N-]1)C1(C(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 1, 11, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 19, 27, 27, 93, 96, 201, 201, 201, 201, 201, 8, 1, 8, 1, 1, 1, 19, 19, 27, 93, 93, 96, 96, 1, 1, 1, 1, 1, 19, 19, 19, 19] 201 rigid atoms, others: [12, 14, 15, 16, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32]) total number of confs: 530 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036424 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036424 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036424/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036424 Building REAL250005036425 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036425' /scratch/stefan/7916117/working/building/REAL250005036425 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036425 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036425/0 /scratch/stefan/7916117/working/building/REAL250005036425 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1021 `/scratch/stefan/7916117/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CN(CC(=O)NCCC2=NC(=O)O[N-]2)N=N1) `REAL250005036425.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036425 none CC(=O)C1=CN(CC(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 60, 66, 60, 60, 60, 38, 38, 38, 17, 8, 1, 1, 1, 1, 1, 1, 1, 60, 60, 66, 66, 66, 60, 60, 60, 38, 17, 17, 8, 8] 66 rigid atoms, others: [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]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036425 none CC(=O)C1=CN(CC(=O)NCCC2=NC(=O)O[N-]2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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, 1, 1, 1, 1, 5, 9, 9, 9, 25, 25, 60, 60, 60, 60, 60, 1, 1, 6, 6, 6, 1, 5, 5, 9, 25, 25, 25, 25] 66 rigid atoms, others: [1, 3, 4, 5, 6, 18, 19, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036425 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036425 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036425/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036425 Building REAL250005036426 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036426' /scratch/stefan/7916117/working/building/REAL250005036426 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036426 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036426/0 /scratch/stefan/7916117/working/building/REAL250005036426 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1022 `/scratch/stefan/7916117/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036426.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036426 none CC(C)C[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 197, 201, 151, 151, 151, 151, 51, 149, 51, 51, 19, 9, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 197, 197, 151, 151, 51, 19, 19, 9, 9] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 748 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: REAL250005036426 none CC(C)C[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 5, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 60, 63, 151, 151, 151, 151, 151, 6, 6, 6, 6, 6, 6, 6, 5, 5, 1, 1, 12, 60, 60, 63, 63] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 377 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036426 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036426 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036426/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036426 Building REAL250005036427 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036427' /scratch/stefan/7916117/working/building/REAL250005036427 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036427 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036427/0 /scratch/stefan/7916117/working/building/REAL250005036427 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1023 `/scratch/stefan/7916117/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(CCCC2)N1) `REAL250005036427.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036427 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(CCCC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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] 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: [12, 1, 12, 12, 56, 85, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 56, 56, 85, 85, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 123 rigid atoms, others: [32, 1, 34, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 426 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036427 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC2=C(CCCC2)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 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] 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: [65, 65, 23, 8, 1, 1, 1, 1, 1, 1, 1, 65, 123, 123, 123, 123, 123, 123, 123, 123, 65, 23, 23, 8, 8, 123, 123, 123, 123, 123, 123, 123, 123, 123, 123] 123 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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 /scratch/stefan/7916117/working/building/REAL250005036427 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036427 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036427/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036427 Building REAL250005036428 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036428' /scratch/stefan/7916117/working/building/REAL250005036428 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036428 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036428/0 /scratch/stefan/7916117/working/building/REAL250005036428 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1024 `/scratch/stefan/7916117/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1CCC(=O)N1)NCCC1=NC(=O)O[N-]1) `REAL250005036428.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036428 none O=C(CCC1CCC(=O)N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 5, 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: [46, 46, 46, 142, 143, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 174, 174, 201, 201, 201, 201, 201, 201, 46, 17, 17, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 958 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036428 none O=C(CCC1CCC(=O)N1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 9, 5, 1, 1, 1, 1, 1, 1, 1, 39, 39, 110, 112, 201, 201, 201, 201, 201, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 39, 110, 110, 112, 112] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 33, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036428 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036428 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036428/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036428 Building REAL250005036429 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036429' /scratch/stefan/7916117/working/building/REAL250005036429 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036429 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036429/0 /scratch/stefan/7916117/working/building/REAL250005036429 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1025 `/scratch/stefan/7916117/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=C(O)C(F)=C1)NCCC1=NC(=O)O[N-]1) `REAL250005036429.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036429 none O=C(CC1=CC=C(O)C(F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 1, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 126, 201, 201, 201, 201, 201, 201, 201, 17, 8, 1, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 402, 201, 53, 17, 17, 8, 8] 402 rigid atoms, others: [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]) total number of confs: 1029 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036429 none O=C(CC1=CC=C(O)C(F)=C1)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 1, 15, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 75, 84, 201, 201, 201, 201, 201, 6, 6, 1, 1, 2, 1, 15, 75, 75, 84, 84] 402 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 25] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 26, 27, 28, 29, 30]) total number of confs: 515 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036429 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036429 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036429/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036429 Building REAL250005036430 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036430' /scratch/stefan/7916117/working/building/REAL250005036430 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036430 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036430/0 /scratch/stefan/7916117/working/building/REAL250005036430 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1026 `/scratch/stefan/7916117/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NN=C1) `REAL250005036430.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036430 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 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: [7, 1, 7, 7, 49, 85, 162, 162, 162, 162, 162, 1, 1, 1, 1, 1, 1, 1, 7, 49, 49, 85, 85, 1, 1, 1] 162 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22]) 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: REAL250005036430 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC(=O)NN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 8, 8, 1, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 6, 4, 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: [63, 63, 23, 8, 1, 1, 1, 1, 1, 1, 1, 63, 162, 162, 162, 162, 162, 162, 63, 23, 23, 8, 8, 162, 162, 162] 162 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036430 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036430 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036430/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036430 Building REAL250005036431 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036431' /scratch/stefan/7916117/working/building/REAL250005036431 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036431 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036431/0 /scratch/stefan/7916117/working/building/REAL250005036431 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1027 `/scratch/stefan/7916117/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[Si](C)(C)CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036431.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036431 none C[Si](C)(C)CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'Si', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 24, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 201, 201, 201, 179, 169, 39, 39, 39, 15, 7, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 39, 15, 15, 7, 7] 201 rigid atoms, others: [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, 36, 37]) total number of confs: 1101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036431 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036431 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036431/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036431 Building REAL250005036432 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036432' /scratch/stefan/7916117/working/building/REAL250005036432 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036432 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036432/0 /scratch/stefan/7916117/working/building/REAL250005036432 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1028 `/scratch/stefan/7916117/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=NC=CN2C1) `REAL250005036432.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036432 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=NC=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 8, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 70, 106, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 70, 70, 106, 106, 1, 1, 1, 1, 1, 1, 1, 1, 1] 178 rigid atoms, others: [32, 1, 33, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 558 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: REAL250005036432 none O=C(NCCC1=NC(=O)O[N-]1)C1CCC2=NC=CN2C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 8, 1, 1, 8, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [97, 97, 24, 8, 1, 1, 1, 1, 1, 1, 1, 97, 178, 178, 178, 178, 178, 178, 178, 178, 96, 24, 24, 8, 8, 178, 178, 178, 178, 178, 178, 178, 178, 178] 178 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 546 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036432 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036432 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036432/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036432 Building REAL250005036433 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036433' /scratch/stefan/7916117/working/building/REAL250005036433 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036433 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036433/0 /scratch/stefan/7916117/working/building/REAL250005036433 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1029 `/scratch/stefan/7916117/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC=C1[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036433.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036433 none CN1C=NC=C1[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 59, 67, 161, 161, 161, 161, 161, 7, 7, 7, 7, 7, 1, 1, 13, 59, 59, 67, 67] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 27, 28] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) 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: REAL250005036433 none CN1C=NC=C1[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 46, 46, 46, 133, 138, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 7, 7, 46, 133, 133, 138, 138] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 625 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036433 none CN1C=NC=C1[C@@H]1C[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 161, 161, 161, 161, 59, 161, 59, 59, 19, 9, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 161, 161, 59, 19, 19, 9, 9] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 550 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036433 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036433 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036433/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036433 Building REAL250005036434 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036434' /scratch/stefan/7916117/working/building/REAL250005036434 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036434 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036434/0 /scratch/stefan/7916117/working/building/REAL250005036434 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1030 `/scratch/stefan/7916117/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1CCCCC1(F)F) `REAL250005036434.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036434 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCCC1(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 69, 107, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 12, 69, 69, 107, 107, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23]) 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: REAL250005036434 none O=C(NCCC1=NC(=O)O[N-]1)C1CCCCC1(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 24, 8, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 201, 201, 201, 101, 25, 25, 8, 8, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036434 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036434 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036434/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036434 Building REAL250005036435 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036435' /scratch/stefan/7916117/working/building/REAL250005036435 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036435 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036435/0 /scratch/stefan/7916117/working/building/REAL250005036435 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1031 `/scratch/stefan/7916117/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1C) `REAL250005036435.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036435 none CC1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 196, 83, 83, 83, 24, 8, 1, 1, 1, 1, 1, 1, 1, 196, 196, 196, 196, 196, 196, 196, 196, 196, 196, 196, 196, 83, 24, 24, 8, 8, 196, 196, 196, 196, 196, 196] 196 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 599 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036435 none CC1CCC(C(=O)NCCC2=NC(=O)O[N-]2)CC1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 75, 120, 196, 196, 196, 196, 196, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 12, 75, 75, 120, 120, 1, 1, 1, 1, 1, 1] 196 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 33, 34, 16, 17, 18, 35, 22, 23, 24, 25, 26, 27, 37, 36] set([32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 28, 29, 30, 31]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036435 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036435 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036435/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036435 Building REAL250005036436 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036436' /scratch/stefan/7916117/working/building/REAL250005036436 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036436 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036436/0 /scratch/stefan/7916117/working/building/REAL250005036436 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1032 `/scratch/stefan/7916117/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@@H]1OCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036436.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036436 none C=C[C@@H]1OCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 63, 201, 63, 63, 19, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 63, 19, 19, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 588 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036436 none C=C[C@@H]1OCC[C@H]1C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 48, 55, 201, 201, 201, 201, 201, 9, 9, 9, 1, 1, 1, 1, 9, 48, 48, 55, 55] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31]) total number of confs: 411 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036436 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036436 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036436/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036436 Building REAL250005036437 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036437' /scratch/stefan/7916117/working/building/REAL250005036437 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036437 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036437/0 /scratch/stefan/7916117/working/building/REAL250005036437 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1033 `/scratch/stefan/7916117/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(F)=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1F) `REAL250005036437.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036437 none CC1=CC(F)=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 115, 31, 31, 31, 13, 7, 1, 1, 1, 1, 1, 1, 1, 173, 201, 201, 201, 201, 201, 201, 115, 115, 31, 13, 13, 7, 7, 201] 201 rigid atoms, others: [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]) total number of confs: 643 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036437 none CC1=CC(F)=C(CC(=O)NCCC2=NC(=O)O[N-]2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 7, 36, 36, 36, 113, 115, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 7, 7, 36, 113, 113, 115, 115, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 18, 19, 20, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 597 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036437 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036437 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036437/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036437 Building REAL250005036438 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036438' /scratch/stefan/7916117/working/building/REAL250005036438 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036438 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036438/0 /scratch/stefan/7916117/working/building/REAL250005036438 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1034 `/scratch/stefan/7916117/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1COCCC1CC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036438.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036438 none COC1COCCC1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 200, 200, 200, 200, 200, 200, 176, 60, 60, 60, 18, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 200, 200, 200, 200, 200, 200, 200, 176, 176, 60, 18, 18, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 763 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036438 none COC1COCCC1CC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 26, 26, 26, 99, 108, 200, 200, 200, 200, 200, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 99, 99, 108, 108] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036438 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036438 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036438/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036438 Building REAL250005036439 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036439' /scratch/stefan/7916117/working/building/REAL250005036439 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036439 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036439/0 /scratch/stefan/7916117/working/building/REAL250005036439 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1035 `/scratch/stefan/7916117/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1CCCC1C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036439.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036439 none CCCC1CCCC1C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 136, 136, 136, 136, 136, 48, 48, 48, 18, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 184, 184, 136, 136, 136, 136, 136, 136, 136, 136, 48, 18, 18, 8, 8] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 798 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: REAL250005036439 none CCCC1CCCC1C(=O)NCCC1=NC(=O)O[N-]1 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.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 50, 136, 136, 136, 136, 136, 6, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 50, 50] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38]) total number of confs: 332 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036439 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036439 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036439/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036439 Building REAL250005036440 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036440' /scratch/stefan/7916117/working/building/REAL250005036440 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036440 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036440/0 /scratch/stefan/7916117/working/building/REAL250005036440 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1036 `/scratch/stefan/7916117/working/3D/1036' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl) `REAL250005036440.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036440 none CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 86, 86, 86, 24, 8, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 164, 86, 24, 24, 8, 8] 164 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036440 none CN1N=CC(C(=O)NCCC2=NC(=O)O[N-]2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 38, 71, 164, 164, 164, 164, 164, 1, 1, 2, 2, 2, 1, 7, 38, 38, 71, 71] 164 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 21] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 22, 23, 24, 25, 26]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036440 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036440 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036440/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036440 Building REAL250005036441 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036441' /scratch/stefan/7916117/working/building/REAL250005036441 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036441 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036441/0 /scratch/stefan/7916117/working/building/REAL250005036441 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1037 `/scratch/stefan/7916117/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)(F)F)N1) `REAL250005036441.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036441 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)(F)F)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 15, 15, 15, 8, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [13, 1, 13, 13, 63, 90, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13, 63, 63, 90, 90, 1, 1, 1] 144 rigid atoms, others: [1, 11, 12, 13, 14, 15, 19, 25, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 20, 21, 22, 23, 24]) total number of confs: 459 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036441 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=C(C(F)(F)F)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 5, 15, 15, 15, 8, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [81, 81, 23, 8, 1, 1, 1, 1, 1, 1, 1, 81, 144, 144, 144, 144, 144, 144, 144, 144, 81, 23, 23, 8, 8, 144, 144, 144] 144 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 353 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036441 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036441 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036441/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036441 Building REAL250005036442 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036442' /scratch/stefan/7916117/working/building/REAL250005036442 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036442 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036442/0 /scratch/stefan/7916117/working/building/REAL250005036442 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1038 `/scratch/stefan/7916117/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=NOC(C(=O)NCCC2=NC(=O)O[N-]2)=C1) `REAL250005036442.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036442 none CCOC1=NOC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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, 192, 141, 141, 140, 140, 82, 82, 82, 24, 8, 1, 1, 1, 1, 1, 1, 1, 141, 201, 201, 201, 201, 201, 81, 24, 24, 8, 8, 141] 201 rigid atoms, others: [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]) total number of confs: 509 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036442 none CCOC1=NOC(C(=O)NCCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [19, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 32, 40, 140, 141, 140, 141, 141, 1, 20, 20, 20, 19, 19, 6, 31, 31, 40, 40, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 18, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036442 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036442 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036442/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036442 Building REAL250005036443 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036443' /scratch/stefan/7916117/working/building/REAL250005036443 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036443 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036443/0 /scratch/stefan/7916117/working/building/REAL250005036443 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1039 `/scratch/stefan/7916117/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CCC(=O)NCCC1=NC(=O)O[N-]1)[N+](=O)[O-]) `REAL250005036443.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036443 none CC(C)(CCC(=O)NCCC1=NC(=O)O[N-]1)[N+](=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 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, 6, 4, 7, 7, 7, 7, 7, 5, 3, 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: [199, 163, 200, 163, 61, 61, 61, 17, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 199, 201, 200, 201, 163, 163, 163, 163, 61, 17, 17, 8, 8] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 865 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036443 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036443 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036443/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036443 Building REAL250005036444 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036444' /scratch/stefan/7916117/working/building/REAL250005036444 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036444 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036444/0 /scratch/stefan/7916117/working/building/REAL250005036444 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1040 `/scratch/stefan/7916117/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036444.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036444 none CC(C)(C)C(=O)CCCC(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 201, 201, 148, 186, 98, 117, 41, 41, 41, 8, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 138, 131, 131, 118, 118, 40, 9, 8, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 994 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036444 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036444 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036444/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036444 Building REAL250005036445 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036445' /scratch/stefan/7916117/working/building/REAL250005036445 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036445 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036445/0 /scratch/stefan/7916117/working/building/REAL250005036445 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1041 `/scratch/stefan/7916117/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N1) `REAL250005036445.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036445 none NC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 130, 201, 130, 130, 130, 65, 65, 65, 22, 8, 1, 1, 1, 1, 1, 1, 1, 130, 201, 201, 130, 130, 64, 22, 22, 8, 8, 130] 201 rigid atoms, others: [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]) 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: REAL250005036445 none NC(=O)C1=CC=C(C(=O)NCCC2=NC(=O)O[N-]2)N1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 8, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 12, 12, 12, 52, 76, 130, 130, 130, 130, 130, 1, 5, 5, 1, 1, 12, 52, 52, 76, 76, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 18, 21, 22, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 23, 24, 25, 26, 27]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036445 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036445 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036445/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036445 Building REAL250005036446 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036446' /scratch/stefan/7916117/working/building/REAL250005036446 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036446 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036446/0 /scratch/stefan/7916117/working/building/REAL250005036446 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1042 `/scratch/stefan/7916117/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CNC2=CC=N1) `REAL250005036446.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036446 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CNC2=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 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: [12, 1, 12, 12, 55, 74, 167, 167, 167, 167, 167, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 55, 55, 74, 74, 1, 1, 1, 1, 1] 167 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24]) total number of confs: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036446 none O=C(NCCC1=NC(=O)O[N-]1)C1=C2C=CNC2=CC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 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: [93, 93, 24, 8, 1, 1, 1, 1, 1, 1, 1, 93, 167, 167, 167, 167, 167, 167, 167, 167, 93, 24, 24, 8, 8, 167, 167, 167, 167, 167] 167 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036446 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036446 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036446/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036446 Building REAL250005036447 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036447' /scratch/stefan/7916117/working/building/REAL250005036447 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036447 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036447/0 /scratch/stefan/7916117/working/building/REAL250005036447 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1043 `/scratch/stefan/7916117/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1) `REAL250005036447.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036447 none N#CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 142, 65, 66, 66, 21, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 65, 22, 22, 8, 8, 142] 142 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24]) 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: REAL250005036447 none N#CC1=CC(C(=O)NCCC2=NC(=O)O[N-]2)=CS1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 14, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 37, 61, 142, 142, 142, 142, 142, 1, 1, 1, 5, 37, 37, 61, 61, 1] 142 rigid atoms, others: [0, 1, 2, 3, 4, 5, 16, 17, 18, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036447 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036447 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036447/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036447 Building REAL250005036448 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036448' /scratch/stefan/7916117/working/building/REAL250005036448 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036448 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036448/0 /scratch/stefan/7916117/working/building/REAL250005036448 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1044 `/scratch/stefan/7916117/working/3D/1044' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1CCCC2) `REAL250005036448.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036448 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 10, 50, 82, 179, 179, 179, 179, 179, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 50, 50, 82, 82, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 179 rigid atoms, others: [1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25]) total number of confs: 500 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036448 none O=C(NCCC1=NC(=O)O[N-]1)C1=CC=CC2=C1CCCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [89, 89, 23, 8, 1, 1, 1, 1, 1, 1, 1, 89, 179, 179, 179, 179, 179, 179, 179, 179, 179, 89, 24, 24, 8, 8, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179] 179 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036448 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036448 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036448/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036448 Building REAL250005036449 mkdir: created directory `/scratch/stefan/7916117/working/building/REAL250005036449' /scratch/stefan/7916117/working/building/REAL250005036449 /scratch/stefan/7916117/working /scratch/stefan/7916117 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005036449 mkdir: created directory `0' /scratch/stefan/7916117/working/building/REAL250005036449/0 /scratch/stefan/7916117/working/building/REAL250005036449 /scratch/stefan/7916117/working /scratch/stefan/7916117 Protomer 0 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7916117/working/3D/1045 `/scratch/stefan/7916117/working/3D/1045' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1) `REAL250005036449.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005036449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916117/working/building/REAL250005036449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005036449 none COC(CC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [176, 155, 51, 150, 201, 201, 201, 201, 201, 201, 51, 51, 8, 8, 1, 1, 1, 1, 1, 1, 1, 176, 176, 176, 155, 201, 201, 201, 201, 201, 201, 201, 50, 9, 8, 8, 8] 201 rigid atoms, others: [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]) 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: REAL250005036449 none COC(CC1=CC=CC=C1)C(=O)NCCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 5, 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: [19, 9, 3, 1, 1, 1, 1, 1, 1, 1, 9, 36, 36, 36, 102, 102, 201, 201, 201, 201, 201, 19, 19, 19, 9, 3, 3, 1, 1, 1, 1, 1, 36, 102, 102, 102, 102] 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]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916117/working/building/REAL250005036449 /scratch/stefan/7916117/working /scratch/stefan/7916117 Finished preparing REAL250005036449 Recording results /scratch/stefan/7916117/working /scratch/stefan/7916117 Appending to /scratch/stefan/7916117/finished/xaaaaao.* 0: /scratch/stefan/7916117/working/building/REAL250005036449/0.* Removing working files in /scratch/stefan/7916117/working/building/REAL250005036449 /scratch/stefan/7916117 Compressing combined databse files /scratch/stefan/7916117/finished/xaaaaao.db2.gz /scratch/stefan/7916117/finished/xaaaaao.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7916117/finished) ======================================================= Finalizing... removed `/scratch/stefan/7916117/working/3D/1046' removed directory: `/scratch/stefan/7916117/working/3D' `/scratch/stefan/7916117/working/protonate' -> `/scratch/stefan/7916117/archive' `/scratch/stefan/7916117/working/input-smiles.ism' -> `/scratch/stefan/7916117/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7916117/working/building' rmdir: removing directory, `/scratch/stefan/7916117/working' ls: No match. ls: No match.