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/7901146/working' mkdir: created directory `/scratch/stefan/7901146/working/protonate' Storing results in /scratch/stefan/7901146/finished Working in /scratch/stefan/7901146/working /scratch/stefan/7901146/working /scratch/stefan/7901146 /scratch/stefan/7901146/working/protonate /scratch/stefan/7901146/working /scratch/stefan/7901146 Precomputing protomers for all compounds (pH: 7.4) ph 7.4: 40 protomers created Coalesing and merging protomers 37 protomers generated for 35 compounds Checking for new stereocenters and expanding 37 protomers after new stereo-center expansion /scratch/stefan/7901146/working /scratch/stefan/7901146 Bulk generating 3D conformations all protomers in /scratch/stefan/7901146/working/3D mkdir: created directory `/scratch/stefan/7901146/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7901146/working/protonate/xaaaaae_worked-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' 38 3D conformations generated for 35 compounds Building REAL300025554507 mkdir: created directory `/scratch/stefan/7901146/working/building' mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554507' /scratch/stefan/7901146/working/building/REAL300025554507 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554507 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554507/0 /scratch/stefan/7901146/working/building/REAL300025554507 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/1 `/scratch/stefan/7901146/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNS(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025554507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554507 none CCNS(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 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, 197, 137, 97, 137, 137, 97, 137, 137, 97, 27, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 134, 137, 201, 201, 201, 201, 201, 197, 137, 137, 97, 97, 26, 8, 8, 137, 137] 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: 1038 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554507 none CCNS(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 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, 3, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 15, 15, 15, 29, 137, 137, 137, 137, 137, 1, 1, 11, 11, 11, 11, 11, 3, 1, 1, 7, 7, 15, 29, 29, 1, 1] 201 rigid atoms, others: [3, 36, 37, 6, 7, 8, 9, 10, 21, 22, 29, 30] set([0, 1, 2, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554507 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554507 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 mkdir: created directory `/scratch/stefan/7901146/finished' Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554507/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554507 Building REAL300025554508 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554508' /scratch/stefan/7901146/working/building/REAL300025554508 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025554508 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554508/0 /scratch/stefan/7901146/working/building/REAL300025554508 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/2 `/scratch/stefan/7901146/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(I)=C1[O-]) `REAL300025554508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554508 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(I)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 18, 1, 12, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [10, 1, 10, 10, 38, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 1, 10, 38, 38, 1, 1, 1] 63 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554508 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(I)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 18, 1, 12, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 46, 63, 63, 63, 63, 63, 63, 63, 46, 8, 8, 63, 63, 63] 63 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554508 /scratch/stefan/7901146/working /scratch/stefan/7901146 mkdir: created directory `1' /scratch/stefan/7901146/working/building/REAL300025554508/1 /scratch/stefan/7901146/working/building/REAL300025554508 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/3 `/scratch/stefan/7901146/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(I)=C1O) `REAL300025554508.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025554508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554508 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(I)=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 18, 1, 12, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 33, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 10, 33, 33, 1, 1, 1, 2] 138 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 24]) total number of confs: 175 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: REAL300025554508 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(I)=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 18, 1, 12, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 8, 1, 1, 1, 1, 1, 1, 1, 42, 69, 69, 69, 69, 69, 69, 69, 41, 8, 8, 69, 69, 68, 138] 138 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 294 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554508 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554508 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 1: /scratch/stefan/7901146/working/building/REAL300025554508/1.* 0: /scratch/stefan/7901146/working/building/REAL300025554508/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554508 Building REAL300025554509 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554509' /scratch/stefan/7901146/working/building/REAL300025554509 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554509 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554509/0 /scratch/stefan/7901146/working/building/REAL300025554509 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/4 `/scratch/stefan/7901146/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1SCC1CCCC1) `REAL300025554509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554509 none O=C(NCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1SCC1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 57, 109, 105, 126, 201, 201, 201, 201, 201, 57, 57, 57, 57, 57, 57, 57, 57, 18, 5, 1, 1, 1, 1, 1, 1, 109, 126, 126, 57, 57, 57, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 497 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554509 none O=C(NCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1SCC1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 57, 57, 57, 57, 7, 15, 15, 1, 1, 1, 25, 25, 57, 57, 57, 57, 57, 57, 57, 57, 57] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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: REAL300025554509 none O=C(NCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1SCC1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 20, 68, 68, 68, 68, 68, 60, 68, 68, 68, 122, 163, 201, 201, 201, 201, 19, 8, 8, 68, 68, 68, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554509 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554509 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554509/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554509 Building REAL300025554510 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554510' /scratch/stefan/7901146/working/building/REAL300025554510 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554510 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554510/0 /scratch/stefan/7901146/working/building/REAL300025554510 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/5 `/scratch/stefan/7901146/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1SC1CCCC1) `REAL300025554510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554510 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1SC1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 14, 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, 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: [66, 24, 66, 66, 104, 201, 201, 201, 201, 201, 24, 24, 24, 24, 24, 24, 7, 1, 1, 1, 1, 1, 1, 66, 104, 104, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28]) total number of confs: 501 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554510 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1SC1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 14, 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, 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, 22, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 7, 22, 22, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 219 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554510 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1SC1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 14, 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, 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: [25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 26, 96, 96, 96, 46, 96, 96, 96, 185, 201, 201, 201, 201, 25, 8, 8, 96, 96, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 576 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554510 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554510 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554510/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554510 Building REAL300025554511 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554511' /scratch/stefan/7901146/working/building/REAL300025554511 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554511 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554511/0 /scratch/stefan/7901146/working/building/REAL300025554511 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/6 `/scratch/stefan/7901146/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025554511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554511 none CNS(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 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, 101, 201, 201, 101, 201, 201, 101, 35, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 184, 201, 201, 201, 201, 201, 201, 201, 101, 101, 34, 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]) total number of confs: 1294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554511 none CNS(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 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, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 15, 15, 15, 47, 201, 201, 201, 201, 201, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 15, 47, 47, 1, 1] 201 rigid atoms, others: [33, 2, 5, 6, 7, 8, 9, 34, 20, 21, 26, 27] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554511 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554511 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554511/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554511 Building REAL300025554512 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554512' /scratch/stefan/7901146/working/building/REAL300025554512 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554512 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554512/0 /scratch/stefan/7901146/working/building/REAL300025554512 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/7 `/scratch/stefan/7901146/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC1=C(Cl)C=CC=C1Cl)C(=O)NCC1=NC(=O)O[N-]1) `REAL300025554512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554512 none CC(=CC1=C(Cl)C=CC=C1Cl)C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', '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, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 38, 83, 83, 83, 83, 83, 83, 83, 83, 83, 37, 37, 8, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 37, 8, 8] 83 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: 245 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: REAL300025554512 none CC(=CC1=C(Cl)C=CC=C1Cl)C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'N.am', '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, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 45, 83, 83, 83, 83, 83, 2, 2, 2, 2, 1, 1, 1, 12, 45, 45] 83 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 222 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554512 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554512 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554512/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554512 Building REAL300025554513 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554513' /scratch/stefan/7901146/working/building/REAL300025554513 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554513 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554513/0 /scratch/stefan/7901146/working/building/REAL300025554513 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/8 `/scratch/stefan/7901146/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025554513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554513 none CC1=CC(Br)=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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: [5, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 25, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 24, 8, 8, 63] 63 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: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554513 none CC1=CC(Br)=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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: [5, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 27, 63, 63, 63, 63, 63, 1, 2, 2, 2, 1, 1, 7, 27, 27, 1] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17, 21, 22, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 23, 24, 25]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554513 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554513 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554513/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554513 Building REAL300025554514 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554514' /scratch/stefan/7901146/working/building/REAL300025554514 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554514 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554514/0 /scratch/stefan/7901146/working/building/REAL300025554514 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/9 `/scratch/stefan/7901146/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C=C1F) `REAL300025554514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554514 none CC(C(=O)NCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 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] 0 hydrogens 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, 42, 42, 42, 107, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 8, 8, 42, 107, 107, 1, 1, 1] 201 rigid atoms, others: [1, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 534 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554514 none CC(C(=O)NCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 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] 0 hydrogens 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, 47, 46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 148, 148, 148, 46, 8, 8, 201, 201, 201] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 613 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554514 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554514 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554514/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554514 Building REAL300025554515 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554515' /scratch/stefan/7901146/working/building/REAL300025554515 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554515 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554515/0 /scratch/stefan/7901146/working/building/REAL300025554515 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/10 `/scratch/stefan/7901146/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2C(F)(F)F)C=C1) `REAL300025554515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554515 none O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [37, 7, 37, 37, 76, 145, 145, 145, 145, 145, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 37, 76, 76, 1, 1, 1, 1, 7, 7] 145 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33]) total number of confs: 359 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554515 none O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 32, 96, 96, 96, 95, 95, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 7, 7, 7, 1, 1, 12, 32, 32, 7, 7, 1, 7, 1, 1] 145 rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 210 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554515 none O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 8, 1, 1, 1, 1, 1, 1, 1, 46, 96, 96, 96, 145, 145, 103, 145, 145, 145, 145, 145, 145, 96, 96, 45, 8, 8, 145, 145, 96, 145, 96, 95] 145 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554515 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554515 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554515/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554515 Building REAL300025554516 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554516' /scratch/stefan/7901146/working/building/REAL300025554516 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554516 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554516/0 /scratch/stefan/7901146/working/building/REAL300025554516 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/11 `/scratch/stefan/7901146/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)C1=CC=C(Cl)C=C1)C(=O)NCC1=NC(=O)O[N-]1) `REAL300025554516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554516 none CC(CC(=O)C1=CC=C(Cl)C=C1)C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [78, 26, 78, 124, 186, 186, 201, 201, 201, 201, 201, 201, 25, 26, 8, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 124, 124, 201, 201, 201, 201, 26, 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]) total number of confs: 768 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554516 none CC(CC(=O)C1=CC=C(Cl)C=C1)C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [35, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 35, 94, 94, 94, 123, 201, 201, 201, 201, 201, 35, 35, 35, 35, 21, 21, 1, 1, 1, 1, 94, 123, 123] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 589 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554516 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554516 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554516/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554516 Building REAL300025554517 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554517' /scratch/stefan/7901146/working/building/REAL300025554517 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554517 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554517/0 /scratch/stefan/7901146/working/building/REAL300025554517 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/12 `/scratch/stefan/7901146/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1SC1=CC=C(Cl)C=C1) `REAL300025554517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554517 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1SC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 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: [63, 21, 63, 63, 90, 201, 201, 201, 201, 201, 21, 21, 11, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 63, 90, 90, 21, 21, 21, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30]) total number of confs: 497 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554517 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1SC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 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: [9, 1, 9, 9, 25, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 12, 21, 21, 21, 9, 25, 25, 1, 1, 1, 21, 21, 21, 21] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 226 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554517 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(Cl)C=C1SC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 16, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 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: [29, 28, 8, 1, 1, 1, 1, 1, 1, 1, 29, 86, 86, 52, 86, 86, 86, 86, 201, 201, 201, 201, 201, 201, 201, 28, 8, 8, 86, 86, 86, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554517 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554517 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554517/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554517 Building REAL300025554518 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554518' /scratch/stefan/7901146/working/building/REAL300025554518 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554518 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554518/0 /scratch/stefan/7901146/working/building/REAL300025554518 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/13 `/scratch/stefan/7901146/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2(C(=O)NCC3=NC(=O)O[N-]3)CCC2)C=C1OC) `REAL300025554518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554518 none COC1=CC=C(C2(C(=O)NCC3=NC(=O)O[N-]3)CCC2)C=C1OC 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 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 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, 75, 20, 19, 20, 8, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 144, 144, 144, 201, 201, 201, 201, 144, 144, 19, 8, 8, 75, 75, 75, 75, 75, 75, 144, 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, 40, 41]) total number of confs: 551 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554518 none COC1=CC=C(C2(C(=O)NCC3=NC(=O)O[N-]3)CCC2)C=C1OC 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 4, 5, 5, 1, 1, 1, 8, 8, 8, 18, 75, 75, 75, 75, 75, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 5, 5, 8, 18, 18, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 17, 18, 19, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554518 none COC1=CC=C(C2(C(=O)NCC3=NC(=O)O[N-]3)CCC2)C=C1OC 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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 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 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, 24, 24, 24, 46, 144, 144, 144, 144, 144, 5, 5, 5, 1, 1, 1, 3, 4, 4, 4, 1, 1, 24, 46, 46, 5, 5, 5, 5, 5, 5, 1, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 20, 21, 22, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554518 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554518 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554518/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554518 Building REAL300025554519 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554519' /scratch/stefan/7901146/working/building/REAL300025554519 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554519 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554519/0 /scratch/stefan/7901146/working/building/REAL300025554519 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/14 `/scratch/stefan/7901146/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC(Cl)=CC2=C1OCC2)NCC1=NC(=O)O[N-]1) `REAL300025554519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554519 none O=C(CC1=CC(Cl)=CC2=C1OCC2)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.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, 16, 1, 1, 1, 12, 5, 5, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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: [29, 29, 30, 109, 201, 201, 201, 200, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 201, 30, 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: 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: REAL300025554519 none O=C(CC1=CC(Cl)=CC2=C1OCC2)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.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, 16, 1, 1, 1, 12, 5, 5, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 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, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 93, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 51, 93, 93] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554519 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554519 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554519/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554519 Building REAL300025554520 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554520' /scratch/stefan/7901146/working/building/REAL300025554520 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554520 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554520/0 /scratch/stefan/7901146/working/building/REAL300025554520 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/15 `/scratch/stefan/7901146/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCSC1=CC=C(Cl)C=C1C(=O)NCC1=NC(=O)O[N-]1) `REAL300025554520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554520 none CCCCSC1=CC=C(Cl)C=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.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, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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, 176, 115, 73, 73, 73, 24, 73, 73, 71, 24, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 176, 176, 73, 73, 73, 24, 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: 813 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554520 none CCCCSC1=CC=C(Cl)C=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.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, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [49, 47, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 73, 73, 73, 73, 73, 49, 49, 49, 49, 49, 47, 47, 33, 33, 1, 1, 1, 7, 17, 17] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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/7901146/working/building/REAL300025554520 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554520 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554520/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554520 Building REAL300025554521 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554521' /scratch/stefan/7901146/working/building/REAL300025554521 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554521 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554521/0 /scratch/stefan/7901146/working/building/REAL300025554521 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/16 `/scratch/stefan/7901146/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(C(=O)NCC1=NC(=O)O[N-]1)C1=CC=C(OC)C(OC)=C1) `REAL300025554521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554521 none CCC(CC)(C(=O)NCC1=NC(=O)O[N-]1)C1=CC=C(OC)C(OC)=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 24, 24, 24, 42, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 24, 42, 42, 1, 1, 3, 3, 3, 4, 4, 4, 1] 201 rigid atoms, others: [2, 38, 39, 46, 15, 16, 17, 18, 19, 21, 22, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 309 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554521 none CCC(CC)(C(=O)NCC1=NC(=O)O[N-]1)C1=CC=C(OC)C(OC)=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 90, 35, 90, 92, 34, 35, 8, 1, 1, 1, 1, 1, 1, 1, 90, 151, 151, 151, 151, 201, 151, 151, 201, 151, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 35, 8, 8, 151, 151, 201, 201, 201, 201, 201, 201, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 659 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554521 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554521 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554521/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554521 Building REAL300025554522 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554522' /scratch/stefan/7901146/working/building/REAL300025554522 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554522 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554522/0 /scratch/stefan/7901146/working/building/REAL300025554522 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/17 `/scratch/stefan/7901146/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCC2=NC(=O)O[N-]2)C(SC2=CC=C(Cl)C=C2)=C1) `REAL300025554522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554522 none CC1=CC=C(C(=O)NCC2=NC(=O)O[N-]2)C(SC2=CC=C(Cl)C=C2)=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 14, 1, 1, 1, 1, 16, 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, 6, 4, 7, 7, 7, 7, 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: [21, 21, 21, 21, 21, 21, 65, 65, 65, 90, 201, 201, 201, 201, 201, 6, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 65, 90, 90, 1, 1, 1, 1, 21] 201 rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 454 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554522 none CC1=CC=C(C(=O)NCC2=NC(=O)O[N-]2)C(SC2=CC=C(Cl)C=C2)=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 14, 1, 1, 1, 1, 16, 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, 6, 4, 7, 7, 7, 7, 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: [86, 52, 86, 86, 27, 26, 27, 8, 1, 1, 1, 1, 1, 1, 1, 86, 86, 201, 201, 201, 201, 201, 201, 201, 86, 86, 86, 86, 86, 86, 27, 8, 8, 201, 201, 201, 201, 86] 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: 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: REAL300025554522 none CC1=CC=C(C(=O)NCC2=NC(=O)O[N-]2)C(SC2=CC=C(Cl)C=C2)=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.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 14, 1, 1, 1, 1, 16, 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, 6, 4, 7, 7, 7, 7, 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, 1, 1, 9, 9, 9, 25, 86, 86, 86, 86, 86, 1, 1, 9, 21, 21, 9, 9, 21, 21, 1, 2, 2, 2, 1, 1, 9, 25, 25, 21, 21, 21, 21, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 15, 16, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554522 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554522 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554522/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554522 Building REAL300025554523 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554523' /scratch/stefan/7901146/working/building/REAL300025554523 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554523 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554523/0 /scratch/stefan/7901146/working/building/REAL300025554523 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/18 `/scratch/stefan/7901146/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)CC(C)(C)CC(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025554523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554523 none COC1=CC=C(C(=O)CC(C)(C)CC(=O)NCC2=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 166, 201, 201, 166, 145, 166, 85, 40, 85, 85, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 145, 145, 85, 85, 85, 85, 85, 85, 40, 40, 20, 8, 8, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 935 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554523 none COC1=CC=C(C(=O)CC(C)(C)CC(=O)NCC2=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 7, 7, 15, 33, 33, 33, 52, 95, 95, 95, 110, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 15, 15, 33, 33, 33, 33, 33, 33, 52, 52, 95, 110, 110, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 44, 23, 24, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554523 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554523 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554523/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554523 Building REAL300025554524 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554524' /scratch/stefan/7901146/working/building/REAL300025554524 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025554524 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554524/0 /scratch/stefan/7901146/working/building/REAL300025554524 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/19 `/scratch/stefan/7901146/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)C1=CC=C([O-])C(C(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025554524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554524 none CN(C)S(=O)(=O)C1=CC=C([O-])C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 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, 104, 201, 201, 104, 63, 104, 104, 104, 49, 48, 48, 8, 1, 1, 1, 1, 1, 1, 1, 104, 201, 201, 201, 201, 201, 201, 104, 104, 48, 8, 8, 104] 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]) total number of confs: 833 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554524 none CN(C)S(=O)(=O)C1=CC=C([O-])C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 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: [17, 8, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 25, 104, 104, 104, 104, 104, 1, 18, 18, 18, 18, 18, 18, 1, 1, 10, 25, 25, 1] 201 rigid atoms, others: [34, 3, 6, 7, 8, 9, 10, 11, 12, 22, 29, 30] set([0, 1, 2, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554524 /scratch/stefan/7901146/working /scratch/stefan/7901146 mkdir: created directory `1' /scratch/stefan/7901146/working/building/REAL300025554524/1 /scratch/stefan/7901146/working/building/REAL300025554524 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/20 `/scratch/stefan/7901146/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)C1=CC=C(O)C(C(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025554524.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025554524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554524 none CN(C)S(=O)(=O)C1=CC=C(O)C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 93, 200, 201, 93, 93, 93, 93, 93, 39, 38, 38, 8, 1, 1, 1, 1, 1, 1, 1, 93, 201, 201, 201, 201, 201, 201, 93, 93, 186, 38, 8, 8, 92] 402 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]) total number of confs: 879 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554524 none CN(C)S(=O)(=O)C1=CC=C(O)C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 5, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 18, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 27, 93, 93, 93, 93, 93, 1, 19, 19, 19, 19, 19, 19, 1, 1, 2, 9, 26, 26, 1] 402 rigid atoms, others: [3, 6, 7, 8, 9, 10, 11, 12, 35, 22, 29, 30] set([0, 1, 2, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554524 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554524 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 1: /scratch/stefan/7901146/working/building/REAL300025554524/1.* 0: /scratch/stefan/7901146/working/building/REAL300025554524/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554524 Building REAL300025554525 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554525' /scratch/stefan/7901146/working/building/REAL300025554525 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554525 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554525/0 /scratch/stefan/7901146/working/building/REAL300025554525 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/21 `/scratch/stefan/7901146/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=NC=C(Br)C=C1Br) `REAL300025554525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554525 none O=C(NCC1=NC(=O)O[N-]1)C1=NC=C(Br)C=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 17, 1, 1, 17, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 29, 1, 1] 53 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554525 none O=C(NCC1=NC(=O)O[N-]1)C1=NC=C(Br)C=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 17, 1, 1, 17, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 29, 53, 53, 53, 53, 53, 53, 53, 28, 8, 8, 53, 53] 53 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554525 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554525 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554525/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554525 Building REAL300025554526 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554526' /scratch/stefan/7901146/working/building/REAL300025554526 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554526 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554526/0 /scratch/stefan/7901146/working/building/REAL300025554526 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/22 `/scratch/stefan/7901146/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=C(F)C=CC=C1SC1=CC=C(Cl)C=C1) `REAL300025554526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554526 none O=C(NCC1=NC(=O)O[N-]1)C1=C(F)C=CC=C1SC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 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: [66, 22, 66, 66, 97, 201, 201, 201, 201, 201, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 66, 97, 97, 22, 22, 22, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30]) total number of confs: 477 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554526 none O=C(NCC1=NC(=O)O[N-]1)C1=C(F)C=CC=C1SC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 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: [7, 1, 7, 7, 21, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 13, 14, 22, 22, 7, 21, 21, 1, 1, 1, 22, 22, 22, 22] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 218 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554526 none O=C(NCC1=NC(=O)O[N-]1)C1=C(F)C=CC=C1SC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 15, 1, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 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: [28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 29, 92, 92, 92, 44, 92, 92, 92, 201, 201, 201, 201, 201, 201, 201, 28, 8, 8, 92, 92, 92, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 505 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554526 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554526 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554526/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554526 Building REAL300025554527 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554527' /scratch/stefan/7901146/working/building/REAL300025554527 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554527 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554527/0 /scratch/stefan/7901146/working/building/REAL300025554527 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/23 `/scratch/stefan/7901146/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(OC2CCCC2)N=C1) `REAL300025554527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554527 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(OC2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 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, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 32, 82, 82, 128, 201, 201, 201, 201, 201, 32, 32, 32, 7, 1, 1, 1, 1, 1, 1, 32, 32, 82, 128, 128, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32] 201 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 27, 28, 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, 36]) total number of confs: 540 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554527 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(OC2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 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, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 21, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 9, 32, 32, 32, 32, 1, 1, 5, 21, 21, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1] 201 rigid atoms, others: [1, 36, 10, 11, 12, 13, 14, 20, 21, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554527 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(OC2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 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, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 37, 94, 94, 94, 94, 177, 201, 201, 201, 201, 94, 94, 37, 8, 8, 94, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 410 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554527 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554527 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554527/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554527 Building REAL300025554528 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554528' /scratch/stefan/7901146/working/building/REAL300025554528 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554528 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554528/0 /scratch/stefan/7901146/working/building/REAL300025554528 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/24 `/scratch/stefan/7901146/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC(F)=CC=C1SC1=CC=C(Cl)C=C1) `REAL300025554528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554528 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(F)=CC=C1SC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 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: [61, 21, 61, 61, 87, 201, 201, 201, 201, 201, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 61, 87, 87, 21, 21, 21, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 21, 22, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30]) total number of confs: 452 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554528 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(F)=CC=C1SC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 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: [7, 1, 7, 7, 23, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 9, 12, 21, 21, 7, 23, 23, 1, 1, 1, 21, 21, 21, 21] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 213 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554528 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(F)=CC=C1SC1=CC=C(Cl)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 15, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 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: [26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 27, 84, 84, 84, 52, 84, 84, 84, 201, 201, 201, 201, 201, 201, 201, 26, 8, 8, 84, 83, 84, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 441 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554528 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554528 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554528/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554528 Building REAL300025554529 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554529' /scratch/stefan/7901146/working/building/REAL300025554529 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554529 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554529/0 /scratch/stefan/7901146/working/building/REAL300025554529 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/25 `/scratch/stefan/7901146/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1SC1=CC=CC=C1) `REAL300025554529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554529 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1SC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 14, 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, 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: [65, 23, 65, 65, 88, 201, 201, 201, 201, 201, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 65, 88, 88, 23, 23, 23, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29]) total number of confs: 434 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554529 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1SC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 14, 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, 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: [7, 1, 7, 7, 21, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 9, 23, 23, 7, 21, 21, 1, 1, 1, 23, 23, 13, 23, 23] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) 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: REAL300025554529 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1SC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 14, 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, 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: [24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 25, 80, 80, 80, 49, 80, 80, 80, 201, 201, 201, 201, 201, 201, 25, 8, 8, 80, 80, 80, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554529 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554529 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554529/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554529 Building REAL300025554530 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554530' /scratch/stefan/7901146/working/building/REAL300025554530 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554530 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554530/0 /scratch/stefan/7901146/working/building/REAL300025554530 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/26 `/scratch/stefan/7901146/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(SC2=CC=C(Cl)C=C2)C(C(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025554530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554530 none CC1=CC=C(SC2=CC=C(Cl)C=C2)C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [87, 87, 53, 87, 87, 87, 201, 201, 201, 201, 201, 201, 201, 27, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 201, 201, 201, 201, 27, 8, 8, 87] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 454 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554530 none CC1=CC=C(SC2=CC=C(Cl)C=C2)C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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: [21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 65, 65, 62, 95, 201, 201, 201, 201, 201, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 65, 95, 95, 21] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 12, 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, 34, 35, 36, 37]) total number of confs: 498 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554530 none CC1=CC=C(SC2=CC=C(Cl)C=C2)C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 14, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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, 9, 21, 21, 9, 12, 21, 21, 1, 1, 9, 9, 9, 25, 87, 87, 87, 87, 87, 1, 2, 2, 2, 1, 1, 21, 21, 21, 21, 9, 25, 25, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 13, 14, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554530 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554530 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554530/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554530 Building REAL300025554531 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554531' /scratch/stefan/7901146/working/building/REAL300025554531 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554531 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554531/0 /scratch/stefan/7901146/working/building/REAL300025554531 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/27 `/scratch/stefan/7901146/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(C(=O)NCC2=NC(=O)O[N-]2)CC1) `REAL300025554531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554531 none CC(C)(C)OC(=O)NCC1(C(=O)NCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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, 194, 173, 194, 130, 65, 21, 20, 21, 8, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201, 173, 130, 130, 20, 8, 8, 65, 65, 65, 65] 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: 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: REAL300025554531 none CC(C)(C)OC(=O)NCC1(C(=O)NCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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: [45, 45, 45, 45, 36, 22, 36, 6, 1, 1, 1, 6, 6, 6, 13, 65, 65, 65, 65, 65, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 22, 6, 6, 6, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554531 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554531 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554531/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554531 Building REAL300025554532 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554532' /scratch/stefan/7901146/working/building/REAL300025554532 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554532 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554532/0 /scratch/stefan/7901146/working/building/REAL300025554532 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/28 `/scratch/stefan/7901146/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC2=NC(=O)O[N-]2)N=C(C2=CC=C(Cl)C(Cl)=C2)O1) `REAL300025554532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554532 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)N=C(C2=CC=C(Cl)C(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 37, 37, 36, 94, 160, 160, 160, 160, 160, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 37, 94, 94, 1, 1, 1] 160 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 463 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554532 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)N=C(C2=CC=C(Cl)C(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [128, 127, 57, 56, 57, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 160, 160, 160, 160, 160, 160, 160, 128, 128, 128, 128, 56, 8, 8, 160, 160, 160] 160 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: 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: REAL300025554532 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)N=C(C2=CC=C(Cl)C(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 10, 9, 39, 128, 128, 128, 128, 128, 1, 1, 1, 4, 4, 2, 2, 4, 4, 4, 1, 2, 2, 2, 10, 39, 39, 4, 4, 4] 160 rigid atoms, others: [0, 1, 2, 3, 13, 14, 15, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554532 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554532 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554532/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554532 Building REAL300025554533 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554533' /scratch/stefan/7901146/working/building/REAL300025554533 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554533 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554533/0 /scratch/stefan/7901146/working/building/REAL300025554533 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/29 `/scratch/stefan/7901146/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1SC1=CC=CC=C1) `REAL300025554533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554533 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1SC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 14, 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, 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: [61, 19, 61, 61, 108, 201, 201, 201, 201, 201, 19, 19, 19, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 61, 108, 108, 19, 19, 19, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29]) total number of confs: 508 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554533 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1SC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 14, 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, 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: [9, 1, 9, 9, 29, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 19, 6, 19, 19, 9, 29, 29, 1, 1, 1, 19, 19, 6, 19, 19] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554533 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(F)=C1SC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 15, 1, 14, 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, 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: [34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 35, 109, 109, 109, 109, 109, 109, 109, 201, 201, 201, 201, 201, 201, 34, 8, 8, 109, 109, 109, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554533 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554533 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554533/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554533 Building REAL300025554534 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554534' /scratch/stefan/7901146/working/building/REAL300025554534 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554534 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554534/0 /scratch/stefan/7901146/working/building/REAL300025554534 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/30 `/scratch/stefan/7901146/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCCC1(C)C(=O)NCC1=NC(=O)O[N-]1) `REAL300025554534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554534 none CC(C)(C)OC(=O)N1CCCCC1(C)C(=O)NCC1=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 144, 86, 144, 86, 86, 86, 86, 86, 50, 86, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 163, 163, 163, 163, 163, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 50, 8, 8] 163 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) 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: REAL300025554534 none CC(C)(C)OC(=O)N1CCCCC1(C)C(=O)NCC1=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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 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 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [20, 18, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 20, 86, 86, 86, 86, 86, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 20, 20] 163 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554534 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554534 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554534/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554534 Building REAL300025554535 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554535' /scratch/stefan/7901146/working/building/REAL300025554535 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554535 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554535/0 /scratch/stefan/7901146/working/building/REAL300025554535 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/31 `/scratch/stefan/7901146/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)CCCCC(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025554535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554535 none COC1=CC=C(C(=O)CCCCC(=O)NCC2=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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 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, 193, 201, 201, 193, 90, 193, 78, 78, 74, 13, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 90, 90, 78, 78, 78, 78, 74, 74, 12, 8, 8, 201, 201] 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, 37, 38, 39, 40, 41]) total number of confs: 688 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554535 none COC1=CC=C(C(=O)CCCCC(=O)NCC2=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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 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, 6, 6, 19, 25, 25, 33, 109, 109, 109, 115, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 19, 19, 25, 25, 25, 25, 33, 33, 109, 115, 115, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 41, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554535 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554535 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554535/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554535 Building REAL300025554536 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554536' /scratch/stefan/7901146/working/building/REAL300025554536 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554536 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554536/0 /scratch/stefan/7901146/working/building/REAL300025554536 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/32 `/scratch/stefan/7901146/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCC2=NC(=O)O[N-]2)=C(C2=CC=CC=C2)O1) `REAL300025554536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554536 none CC1=NC(C(=O)NCC2=NC(=O)O[N-]2)=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 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, 6, 4, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 35, 35, 35, 92, 179, 179, 179, 179, 179, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 35, 92, 92, 1, 1, 1, 1, 1] 179 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 470 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554536 none CC1=NC(C(=O)NCC2=NC(=O)O[N-]2)=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 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, 6, 4, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 56, 55, 55, 8, 1, 1, 1, 1, 1, 1, 1, 169, 169, 179, 179, 171, 179, 179, 169, 169, 169, 169, 55, 8, 8, 179, 179, 169, 179, 179] 179 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: 339 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554536 none CC1=NC(C(=O)NCC2=NC(=O)O[N-]2)=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 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, 6, 4, 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 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, 13, 13, 13, 55, 169, 169, 169, 169, 169, 1, 1, 6, 6, 1, 6, 6, 1, 2, 2, 2, 13, 55, 55, 6, 6, 1, 6, 6] 179 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 21] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 365 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554536 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554536 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554536/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554536 Building REAL300025554537 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554537' /scratch/stefan/7901146/working/building/REAL300025554537 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554537 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554537/0 /scratch/stefan/7901146/working/building/REAL300025554537 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/33 `/scratch/stefan/7901146/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)C2=CC=CC=C2C(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025554537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554537 none COC1=CC=C(C(=O)C2=CC=CC=C2C(=O)NCC2=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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, 193, 118, 193, 118, 118, 117, 118, 118, 25, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 118, 118, 118, 118, 24, 8, 8, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 460 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554537 none COC1=CC=C(C(=O)C2=CC=CC=C2C(=O)NCC2=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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, 13, 13, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 118, 118, 118, 118, 118, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 10, 22, 22, 21, 21] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554537 none COC1=CC=C(C(=O)C2=CC=CC=C2C(=O)NCC2=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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, 9, 9, 21, 21, 21, 21, 21, 21, 69, 69, 69, 101, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 69, 101, 101, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554537 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554537 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554537/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554537 Building REAL300025554538 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554538' /scratch/stefan/7901146/working/building/REAL300025554538 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554538 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554538/0 /scratch/stefan/7901146/working/building/REAL300025554538 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/34 `/scratch/stefan/7901146/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025554538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554538 none CC(C)S(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 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, 119, 201, 86, 119, 119, 83, 119, 119, 83, 31, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 114, 119, 201, 201, 201, 201, 201, 201, 201, 119, 119, 83, 83, 31, 8, 8, 119, 119] 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: 1129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554538 none CC(C)S(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 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, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 34, 119, 119, 119, 119, 119, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 6, 6, 15, 34, 34, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 38, 37, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554538 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554538 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554538/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554538 Building REAL300025554539 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554539' /scratch/stefan/7901146/working/building/REAL300025554539 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554539 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554539/0 /scratch/stefan/7901146/working/building/REAL300025554539 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/35 `/scratch/stefan/7901146/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CSC1=NN=C2C=CC=CN21)NCC1=NC(=O)O[N-]1) `REAL300025554539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554539 none O=C(CSC1=NN=C2C=CC=CN21)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', '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, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [30, 30, 31, 97, 191, 201, 201, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 97, 97, 201, 201, 201, 201, 30, 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]) 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: REAL300025554539 none O=C(CSC1=NN=C2C=CC=CN21)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', '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, 1, 8, 8, 1, 1, 1, 1, 1, 8, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [90, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 90, 90, 119, 201, 201, 201, 201, 201, 21, 21, 1, 1, 1, 1, 90, 119, 119] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29]) total number of confs: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554539 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554539 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554539/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554539 Building REAL300025554540 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554540' /scratch/stefan/7901146/working/building/REAL300025554540 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554540 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554540/0 /scratch/stefan/7901146/working/building/REAL300025554540 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/36 `/scratch/stefan/7901146/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2C(F)(F)F)C=C1[O-]) `REAL300025554540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554540 none O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2C(F)(F)F)C=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 56, 56, 111, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 56, 111, 111, 1, 1, 1, 1, 7] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 524 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554540 none O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2C(F)(F)F)C=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 38, 117, 117, 118, 117, 117, 1, 1, 1, 1, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 1, 1, 12, 38, 38, 7, 7, 3, 7, 1] 201 rigid atoms, others: [1, 33, 10, 11, 12, 13, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 253 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554540 none O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2C(F)(F)F)C=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 1, 1, 1, 1, 1, 1, 1, 47, 118, 118, 118, 201, 201, 173, 201, 201, 201, 201, 201, 201, 118, 118, 117, 46, 8, 8, 201, 201, 173, 201, 118] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554540 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554540 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554540/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554540 Building REAL300025554541 mkdir: created directory `/scratch/stefan/7901146/working/building/REAL300025554541' /scratch/stefan/7901146/working/building/REAL300025554541 /scratch/stefan/7901146/working /scratch/stefan/7901146 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025554541 mkdir: created directory `0' /scratch/stefan/7901146/working/building/REAL300025554541/0 /scratch/stefan/7901146/working/building/REAL300025554541 /scratch/stefan/7901146/working /scratch/stefan/7901146 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7901146/working/3D/37 `/scratch/stefan/7901146/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=CC=C(C(=O)NCC3=NC(=O)O[N-]3)S2)O1) `REAL300025554541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025554541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901146/working/building/REAL300025554541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554541 none CC1=CC=C(C2=CC=C(C(=O)NCC3=NC(=O)O[N-]3)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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, 164, 165, 165, 126, 125, 126, 126, 45, 44, 44, 8, 1, 1, 1, 1, 1, 1, 1, 126, 165, 165, 165, 165, 165, 165, 126, 126, 44, 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, 30]) total number of confs: 310 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554541 none CC1=CC=C(C2=CC=C(C(=O)NCC3=NC(=O)O[N-]3)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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: [12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 42, 126, 126, 126, 126, 126, 1, 12, 13, 13, 13, 12, 13, 1, 1, 13, 42, 42] 165 rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025554541 none CC1=CC=C(C2=CC=C(C(=O)NCC3=NC(=O)O[N-]3)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 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, 12, 12, 12, 12, 66, 66, 66, 98, 165, 165, 165, 165, 165, 12, 1, 2, 2, 2, 1, 1, 13, 12, 66, 98, 98] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901146/working/building/REAL300025554541 /scratch/stefan/7901146/working /scratch/stefan/7901146 Finished preparing REAL300025554541 Recording results /scratch/stefan/7901146/working /scratch/stefan/7901146 Appending to /scratch/stefan/7901146/finished/xaaaaae_worked.* 0: /scratch/stefan/7901146/working/building/REAL300025554541/0.* Removing working files in /scratch/stefan/7901146/working/building/REAL300025554541 /scratch/stefan/7901146 Compressing combined databse files /scratch/stefan/7901146/finished/xaaaaae_worked.db2.gz /scratch/stefan/7901146/finished/xaaaaae_worked.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7901146/finished) ======================================================= Finalizing... removed `/scratch/stefan/7901146/working/3D/38' removed directory: `/scratch/stefan/7901146/working/3D' rmdir: removing directory, `/scratch/stefan/7901146/working/building' rmdir: removing directory, `/scratch/stefan/7901146/working' ls: No match. ls: No match.